15 Best Anime of the 2000s

Best Anime in 2000s

The 2000s arrived, continuing the trend of the 1980s and 1990s, a period of anime prosperity.
Unlike the early stage, the 2000s are still fresh in our minds; some well-known anime that began airing in the 2000s are still on the air.

It was during this period that the Sekai-kei genre was born and permeated the world. Sekai-kei is a group of works in which a small problem in the relationship between the protagonist and heroine directly leads to a major abstract problem such as world crisis or the end of the world.

Let’s take a look at some major events of the 2000s, both positive and negative, in Japan, the land of anime, and the world. Japanese saw the year 2000 problem, the release of Nintendo’s GameCube and DS, 2002 FIFA Korea/Japan World Cup, Studio Ghibli’s great film Spirited Away as a winner for the Oscar. Worldwide events in the 2000 include Summer Olympics in Sydney and Athens, the launch of the first iPod and iPhone, the September 11 attacks, Indian Ocean earthquakes and tsunami, Michael Jackson’s sudden death, etc.

For new anime fans and old veterans alike, the 2000s are an essential part of the modern anime story. Today, I’d like to introduce the list of best anime of the 2000s, which includes some of the best of the best that continue to be noted as a Hall of Fame inductee.

15. Death Note

Death Note
Death Note ©大場つぐみ・小畑健/集英社・VAP・マッドハウス・NTV・D.N.ドリームパートナーズ

A supernatural thriller masterpiece Death Note (DEATH NOTE -デスノート-) is a 37-episode anime series that aired from 2006 to 2007, which shocked the manga and anime industry in the 2000s. It’s an adaptation of a manga written by Tsugumi Ohba and illustrated by Takeshi Obata, who are also famous for Bakuman (2018-2012) and Platinum End (2015-2021). The anime series was produced by Madhouse, with Tetsuro Araki as director, who is also known for the latest hit Attack on Titan series.

Death Note revolves around a high school prodigy named Light Yagami, who stumbles upon a mysterious notebook called the Death Note. This notebook, dropped by a rogue Shinigami (god of death) named Ryuk, grants the user the power to kill anyone whose name and face they know. With this deadly power, Light embarks on a twisted journey of justice, aiming to eradicate the world’s criminals and establish himself as a new god. The story intensifies when a famous detective known as ‘L’ begins to investigate the mysterious deaths, setting the stage for a high-stakes game of cat and mouse.

Aired: 2006-2007

Episodes: 37

Studio: Madhouse

The intense psychological and intellectual battle between the dark hero Light Yagami and the detective L has captivated numerous fans since the series began. Death Note, with its portrayal of a struggle between high IQ characters, is often compared to other series such as Hunter x Hunter, which also depict battles of wits.

14. Tokyo Godfathers

Tokyo Godfathers
Tokyo Godfathers © 2003 Satoshi Kon, Mad House and Tokyo Godfathers Committee.

As a distinct departure from the norm, Tokyo Godfathers (東京ゴッドファーザーズ) is a standalone anime film directed by the celebrated Satoshi Kon and produced by the acclaimed Madhouse studio. It is known as his third full-length theatrical movie following Perfect Blue in 1997 and Millennium Actress in 2001. Released in 2003, this film is celebrated for its unique blend of drama, comedy, and mystery elements, coupled with Kon’s characteristic exploration of perception and reality.

The story is centered around three homeless individuals: an alcoholic named Gin, a former drag queen named Hana, and a runaway girl named Miyuki. On Christmas Eve, they discover an abandoned newborn while rummaging through trash. Driven by compassion and a sense of responsibility, they embark on a quest throughout Tokyo to find the baby’s parents, delving into their own haunted pasts along the way. This peculiar journey is a heartwarming tale that reveals the human spirit’s resilience and the miracles of everyday life.

Released: 2003

Runtime: 92 min

Director: Satoshi Kon

Paprika, another brilliant work from the mind of Satoshi Kon released in 2006, is definitely among the standout anime of the 2000s. If you’ve enjoyed Tokyo Godfathers, then Paprika is a must-watch. This mesmerizing psychological thriller delivers a unique visual spectacle, delving deep into the realm of dreams and reality.

13. FLCL


FLCL (フリクリ), pronounced as Fooly Cooly, is a unique blend of coming-of-age drama, science fiction, and surreal comedy. Created by Production I.G and Gainax and released from 2000 to 2001, it’s a highly original six-episode OVA series with its bizarre narrative and unpredictable storytelling. Despite its brevity, it left a significant impact on the anime community for its out-of-the-box style. The director is Kazuya Tsurumaki, who made Neon Genesis Evangelion as a main staff with its director Hideaki Anno.

As for the synopsis, FLCL follows Naota, a 12-year-old boy whose mundane life gets a spin after a Vespa-riding woman named Haruko hits him. With robots emerging from his head and Haruko’s eccentric behavior causing chaos, Naota’s life takes on a new dimension of weirdness. This show is a metaphorical journey representing the turmoil and confusion of adolescence.

Released: 2000-2001

Episodes: 6

Studio: Production I.G/Gainax

The surrealism of FLCL was so profound that when I first watched it, I thought, “I’ve never seen an anime like this before.” It’s a one-of-a-kind work that encapsulates the nostalgic atmosphere of the early 2000s and the delicate nature of boys and girls.

12. Code Geass: Lelouch of the Rebellion

Code Geass: Lelouch of the Rebellion
Code Geass: Lelouch of the Rebellion ©SUNRISE/PROJECT GEASS Character Design ©2006 CLAMP・ST

Code Geass: Lelouch of the Rebellion (コードギアス 反逆のルルーシュ), produced by Sunrise, is a critically acclaimed mecha-themed dark-fantasy anime that originally aired from 2006 to 2008. After the first 25 episodes aired between 2006 and 2007, the second season titled Code Geass: Lelouch of the Rebellion R2 was released with another 25 episodes in 2008. It stands out with its elaborate plot, charismatic characters, and its examination of complex themes like power, morality, and the nature of freedom. There is also a three-part anime movie of Code Geass Lelouch of the Rebellion, followed by the new anime movie Code Geass Lelouch of the Re;surrection in 2019.

In this epic tale of Code Geass, Lelouch vi Britannia, an exiled prince, gains the power of absolute obedience from a mysterious girl named C.C. Armed with this Geass and a deep-seated hatred for the Empire, he embarks on a mission to topple Britannia, all while donning the persona of the masked vigilante Zero. His strategic brilliance and Geass make for a potent combo, leading to intense battles and unexpected twists.

Aired: 2006-2007 (Season 1)/2008 (Season 2)

Episodes: 25 (Season 1)/25 (Season 2)

Studio: Sunrise

11. Howl’s Moving Castle

Howl's Moving Castle
Howl’s Moving Castle © 2004 Studio Ghibli・NDDMT

Howl’s Moving Castle (ハウルの動く城), a Studio Ghibli film released in 2004, is one of the most famous anime movies in the 2000s. It was adapted from Diana Wynne Jones’s novel published in 1986. The film, directed by Hayao Miyazaki, gained international acclaim, was a box office hit, and earned an Oscar nomination for Best Animated Feature. The first half of the story follows the original source material relatively closely, but the latter half deviates significantly, with additions such as a war that was not present in the original. The original author, Jones, has praised this film as being superb.

Sophie, a hatter, leads a simple life until a witch’s curse transforms her into an old woman. Seeking a cure, she stumbles upon the moving castle of the mysterious wizard Howl. Alongside Howl, a sentient fire named Calcifer, and a cast of enchanting characters, Sophie embarks on a magical adventure, changing her life and Howl’s forever. With its blend of whimsy, romance, and anti-war themes, it’s a truly captivating tale.

Released: 2004

Runtime: 119 min

Director: Hayao Miyazaki

When thinking of Studio Ghibli films from the 2000s, several come to mind. Although it did not make this ranking, the 2008 film, Ponyo, is worth mentioning. This is a film that can be enjoyed by both adults and children, and it is definitely worth a watch.

10. Toradora!

Toradora! ©竹宮ゆゆこ/アスキー・メディアワークス/「とらドラ!」製作委員会

Known for its emotionally charged story and complex characters, Toradora! (とらドラ!) is a romantic comedy anime that aired from October 2008 to March 2009. Adapted from the light novel by Yuyuko Takemiya, this 25-episode series was brought to life by J.C.Staff under the direction of Tatsuyuki Nagai with a script by Mari Okada, who are also famous for other renowned works such as Anohana: The Flower We Saw That Day (2011) and The Anthem of the Heart (2015).

The story of Toradora! revolves around two high school students, Ryuji Takasu and Taiga Aisaka, who despite their contrasting personalities and appearances, share a mutual crush on each other’s best friends. As they become closer, they agree to help each other get their respective love interests, but their evolving relationship leads to unexpected situations, creating a heartfelt tale of love and friendship.

Aired: 2008-2009

Episodes: 25

Studio: J.C.Staff


Toradora! is a timeless masterpiece among rom-com anime adaptations from light novels, deserving of being passed down to future generations. It uncovers heartwarming drama within everyday life and has contributed significantly to the recognition of the romantic comedy drama genre. It’s indeed a commendable work of animation.

9. 5 Centimeters per Second

5 Centimeters per Second
5 Centimeters per Second © Makoto Shinkai / CoMix Wave Films

In the 2000s, that world-famous anime director Makoto Shinkai began to rise to prominence. 5 Centimeters per Second (秒速5センチメートル), a poignant anime movie directed by Makoto Shinkai and produced by CoMix Wave Films, won the audience’s heart when it was released in 2007. It is the third theatrical work by Makoto Shinkai following Voices of a Distant Star (2002) and The Place Promised in Our Early Days (2004). It includes three parts: Cherry Blossom (桜花抄), Cosmonaut (コスモナウト) and 5 Centimeters per Second (秒速5センチメートル). Shinkai’s distinctive visual style and storytelling approach resonate throughout the film, resulting in a heartfelt depiction of young love, distance, and time.

Cherry Blossom – It portrays the blossoming love of two elementary school students, Akari and Takaki. Despite being separated due to family circumstances, they maintain a strong bond through letters.

Cosmonaut – Now in high school, Takaki’s story continues, this time from the perspective of Kanae, who harbors an unspoken love for him. She struggles with her feelings and the knowledge that Takaki might still be longing for Akari.

5 Centimeters per Second – In the final segment, Takaki and Akari are now adults leading separate lives. Still marked by their childhood connection, they reflect on their past and the speed at which life moves – 5 Centimeters per Second.

Released: 2007

Runtime: 63 min

Director: Makoto Shinkai

Today, he’s renowned for his massive hits such as Your Name, Weathering with You, and Suzume. However, 5 Centimeters per Second packs a unique charm inherent in his early works. Those who haven’t seen it yet are highly recommended to give it a watch.

8. K-On!

K-On! ©かきふらい・芳文社/桜高軽音部

Kyoto Animation was one of the most influential anime studios of the 2000s, producing numerous quality works. Foremost among them is arguably the best slice-of-life anime, K-On! (けいおん!). It is a beloved band-themed anime by Kyoto Animation, aired from 2009 to 2010, based on Kakifly’s four-panel manga series published from 2007 to 2012. This series centers on a high school light music club, charming audiences with its endearing characters, catchy music, and heartwarming storylines. After the two seasons broadcasted, the series concluded with K-On! The Movie in 2011.

K-On! centers around the members of the light music club at Sakuragaoka High School. Season 1 follows Yui, a clueless girl with no musical experience, as she joins the club and learns to play guitar. The group, including Mio, Ritsu, and Tsumugi, faces the challenges of club activities while forming close bonds. Season 2 deepens their friendship as they balance school life, club activities, and preparations for the school festival. This season also introduces new characters and adds more depth to the girls’ senior year, culminating in a touching graduation ceremony, leaving a profound impact on their younger club mate, Azusa.

Aired: 2009 (Season 1)/2010 (Season 2)

Episodes: 14 (Season 1)/27 (Season 2)

Studio: Kyoto Animation

Even after its broadcast, many other slice-of-life and band-themed anime were born and continue to be created to this day, but it’s difficult to discuss these works without mentioning the K-On! series.

7. Fullmetal Alchemist/Fullmetal Alchemist: Brotherhood

Fullmetal Alchemist: Brotherhood
Fullmetal Alchemist: Brotherhood ©荒川弘/鋼の錬金術師製作委員会

You can’t look back on the 2000s without the outstanding dark-fantasy series Fullmetal Alchemist, which has two different versions of anime adaptation from Hiromu Arakawa’s manga serialized between 2001 and 2010. Fullmetal Alchemist (鋼の錬金術師), the first series released in 2003-2004, is an epic tale that diverges from the manga’s storyline due to it surpassing the publication rate. Nevertheless, it’s still highly revered for its unique take on the characters and plot. In 2009, Fullmetal Alchemist: Brotherhood (鋼の錬金術師 FULLMETAL ALCHEMIST) was released, this time faithfully following the manga’s storyline. Both versions have left an indelible mark on anime history.

Fullmetal Alchemist brings us into the lives of two alchemist brothers, Edward and Alphonse Elric. Driven by a tragic past, they embark on a journey to seek the Philosopher’s Stone. Their mission stems from a disastrous failed attempt to resurrect their deceased mother through alchemy, resulting in Edward losing an arm and a leg, and Alphonse, his entire body. As they delve deeper into their journey, they discover the military’s dark secrets, encounter the deadly Homunculi, and unravel the true nature of the Philosopher’s Stone. The series addresses themes of sacrifice, brotherhood, and the morality of alchemy.

Aired: 2003-2004 (Fullmetal Alchemist)/2009-2010(Fullmetal Alchemist: Brotherhood)

Episodes: 51(Fullmetal Alchemist)/64 (Fullmetal Alchemist: Brotherhood)

Studio: Bones

If you’re planning to watch the Fullmetal Alchemist anime now, I would recommend the second version, Fullmetal Alchemist: Brotherhood. This is because it faithfully follows the storyline of the original manga. Don’t miss out on the greatest journey of the Elric brothers.

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6. Naruto

Naruto ©岸本斉史 スコット/集英社・テレビ東京・ぴえろ

Centered on the journey of Naruto Uzumaki, an orphaned adolescent ninja from the fictional village of Konoha, Naruto (NARUTO -ナルト-) is an iconic anime series based on Masashi Kishimoto’s manga. Produced by Studio Pierrot, the first part debuted in 2002 and concluded in 2007 with 220 episodes. It was followed by the sequel titled Naruto: Shippuden (NARUTO -ナルト- 疾風伝), which contains 500 episodes airing from 2007 to 2017. The series has spawned a franchise with multiple sequels, movies, and a vast array of merchandise.

In Naruto, the titular protsagonist aims to become Hokage, the village’s leader and strongest ninja. Overcoming many trials and forming deep bonds with friends and rivals, Naruto grows from a mischievous prankster into a mature and capable ninja. The series explores themes of friendship, rivalry, redemption, and the devastating consequences of war.

Aired: 2002-2007 (Naruto)/2007-2017 (Naruto: Shippuden)

Episodes: 220 (Naruto)/500 (Naruto: Shippuden)

Studio: Pierrot


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Although the series has continued with Boruto: Naruto Next Generations, where Naruto’s son is the protagonist, the original Naruto remains a symbolic presence in the world of manga and anime. It’s a must-watch masterpiece for all anime fans.

5. Clannad

Clannad ©VisualArt’s/Key/光坂高校演劇部

Clannad is one of the most emotional and heartwarming anime series in the 2000s, produced by Kyoto Animation. Based on a popular visual novel first released in 2004, it consists of two seasons Clannad in 2007-2008 and Clannad After Story in 2008-2009. It seamlessly blends high school life with fantasy elements. Its blend of comedy, drama, romance, and supernatural elements, along with its exceptional character development, have helped it to stand out among other slice-of-life anime.

Clannad centers around Tomoya Okazaki, a jaded high school student who thinks life is dull. His perspective changes when he meets Nagisa Furukawa, a soft-spoken girl repeating her senior year due to illness. He also encounters other remarkable girls, including the strong-willed Kyou Fujibayashi, her gentle twin sister Ryou, and the mysterious Kotomi Ichinose. Each girl has her unique challenges, and Tomoya finds himself helping them, forming close bonds. In the process, he confronts his own issues too, notably his strained relationship with his father and his struggles with personal growth and self-understanding. Through these experiences, Tomoya learns about the importance of family and friendship.

Aired: 2007-2008 (Season 1)/2008-2009 (Season 2)

Episodes: 22 (Season 1)/22 (Season 2)

Studio: Kyoto Animation

Clannad is a profoundly moving series that stays in your heart, it’s often said “Clannad is life”. While Season 1 introduces various captivating characters, personally, Season 2 was more tear-jerking for me. If you want to cry with an anime, choose Clannad first.

4. The Girl Who Leapt Through Time

The Girl Who Leapt Through Time
The Girl Who Leapt Through Time ©「時をかける少女」製作委員会2006

An award-winning anime film, directed by Mamoru Hosoda and produced by Madhouse studio, The Girl Who Leapt Through Time (時をかける少女) is a 2006 adaptation loosely based on Yasutaka Tsutsui’s 1967 novel. Recognized as the Animation of the Year at the 30th Japan Academy Prize, this cherished movie remains impactful. It is categorized as science fiction and slice of life, having the theme of time leap.

Makoto Konno, a high school girl, discovers the ability to leap through time after a peculiar accident. She uses her newfound power for trivial matters, until she realizes the consequences her actions have on the people around her. This realization turns her exciting adventure into a race against time to fix the timeline. The Girl Who Leapt Through Time is also highlighted by two other main characters Chiaki and Kosuke, her close friends.

Released: 2006

Runtime: 98 min

Director: Mamoru Hosoda

Honestly, I tend to rate Mamoru Hosoda’s earlier works including The Girl Who Leapt Through Time and Summer Wars higher than his recent ones such as Mirai and Belle. Among them, The Girl Who Leapt Through Time is an animation based on a wonderful original novel, but it was completely transformed into another masterpiece by Hosoda.

3. Bakemonogatari

Bakemonogatari ©西尾維新/講談社・アニプレックス・シャフト

In the late 2000s, a prominent anime series was born, titled Bakemonogatari (化物語). Bakemonogatari is the first title of the long-running Monogatari Series, which is looked on as one of the best anime series of all time. Created by the collaboration of the highly acclaimed author Nisio Isin and the anime studio SHAFT, it is a unique and mind-bending supernatural drama. Originally a light novel series, it stands out for its distinct art style, dialogue-heavy storytelling, and clever wordplay. Firstly, 12 episodes aired on TV in 2009 and the remaining three episodes were distributed online through 2010. First Season consists of Nisemonogatari and Nekomonogatari (Black) in 2012 in addition to Bakemonogatari.

In Bakemonogatari, a high school student Koyomi Araragi, who barely survived a vampire attack, now finds himself dealing with various “apparitions” – supernatural creatures that are causing issues in his schoolmates’ lives. Throughout the series, he helps several girls: Hitagi Senjogahara, afflicted by a weight crab; Mayoi Hachikuji, a wandering spirit lost in the mortal world; Suruga Kanbaru, cursed by a monkey’s paw; Nadeko Sengoku, possessed by a snake god; and Tsubasa Hanekawa, his class representative dealing with a cat spirit. Each arc unravels their stories, revealing complex motives and emotional struggles, as Koyomi’s relationship with each girl deepens. All the while, Koyomi grapples with his humanity and the lingering effects of his own brush with the supernatural.

Aired: 2009-1010

Episodes: 15

Studio: Shaft

Monogatari Series currently spans three seasons and consists of 100 episodes, which may feel long to some. However, its rollercoaster-like narrative ensures that you’ll breeze through it. Paying attention to each relationship between the characters further enriches the experience. With the original light novel series by Nisio Isin still ongoing, I’m looking forward to future anime adaptations.

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2. Spirited Away

Spirited Away
Spirited Away © 2001 Studio Ghibli・NDDTM

Spirited Away (千と千尋の神隠し) is an award-winning film from Studio Ghibli and Hayao Miyazaki, known for its stunning anime movie, imaginative world-building, and captivating storytelling. It won the Best Animated Feature at the 75th Academy Awards, making it the first and only Japanese film to have won this award until today. It has inspired countless artists worldwide and remains one of the most influential films in the history of animation.

In the story, 10-year-old Chihiro and her parents stumble upon a seemingly abandoned amusement park. After her mother and father are turned into pigs, Chihiro meets the enigmatic Haku, who explains that the park is a resort for supernatural beings who need a break from their time spent in the earthly realm, and she must work there to free herself and her parents. As Chihiro navigates this bizarre world, she encounters an array of outlandish characters and situations, each posing a unique challenge. This breathtaking film explores themes of identity, growing up, and the dichotomy between greed and selflessness.

Released: 2001

Runtime: 124 min

Director: Hayao Miyazaki

I firmly believe that Spirited Away is not only the greatest Studio Ghibli film of the 2000s but also the best in the history of anime movies. It’s a rare piece that can be enjoyed by all generations, from adults to children, and not just experts. Plus, it never gets old no matter how many times you watch it.

1. The Melancholy of Haruhi Suzumiya

The Melancholy of Haruhi Suzumiya
The Melancholy of Haruhi Suzumiya ©2006 谷川 流・いとうのいぢ/SOS団 ©2007,2008,2009 谷川 流・いとうのいぢ/SOS団

Regarded as a groundbreaking anime series, The Melancholy of Haruhi Suzumiya (涼宮ハルヒの憂鬱) took the anime world by storm when it first aired in 2006. Made by Kyoto Animation, the series is renowned for its intricate narratives, relatable characters, unique storytelling techniques, and blend of multiple genres including slice of life, science fiction, and comedy. The show stands as a pillar of 2000s anime, influencing countless works that followed. The unconventional airing order of the episodes, including a rerun season with new episodes mixed in, also sparked a lot of discussions. After the two seasons released, the only anime movie The Disappearance of Haruhi Suzumiya premiered in 2010 (涼宮ハルヒの消失).

Haruhi Suzumiya, a high school girl with the unique ability to alter reality, forms the SOS Brigade to explore supernatural phenomena. Unaware of her powers, her eccentric demands lead to unconventional and hilarious adventures for the club members. Kyon, an unwitting accomplice, becomes the narrative voice, juggling with the club’s wild escapades and a secret: everyone except Haruhi knows about her abilities and they are there to observe and contain her. The anime showcases their day-to-day life, making the mundane surreal, and underpinning it all is the question: what will happen if Haruhi learns the truth about herself?

Aired: 2006 (Season 1)/2009 (Season 2)

Episodes: 14 (Season 1)/14 reruns + 14 new episodes (Season 2)

Studio: Kyoto Animation

Deciding the number one anime of the 2000s is quite a challenge, but all things considered, The Melancholy of Haruhi Suzumiya has been chosen as the best anime in the 2000s. This is not only because it was a work that made anime more widely recognized among a broader audience, but also simply because it was so entertaining. This is one of the reasons it was selected as the best.

Did you enjoy the world of the top-rated anime in the 2000s? There are so many masterpieces of anime born in the 2000s that it may be difficult to watch them all. Nevertheless, the above 15 selected series and movies are still very much worth watching. Try them!

▽Check the lists of the best anime in other decades!▽


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