20 Best Mystery Anime That Will Keep You Guessing

If you’re a fan of mind-bending twists, complex storylines, and the thrill of uncovering secrets, then mystery anime is the perfect genre for you. Whether it’s solving grisly murders, unearthing hidden truths, or navigating psychological puzzles, mystery anime keeps viewers on the edge of their seats with suspense and intrigue. These shows don’t just entertain—they challenge your perception and make you question everything you think you know.

In this article, we’ve compiled a list of the 20 best mystery anime that are guaranteed to keep you guessing until the very end. From classic masterpieces to underrated gems, each of these titles offers a unique blend of suspense, character depth, and plot twists that will leave you hooked from the first episode. Ready to dive into the unknown? Let’s unravel the mystery together.

20. From the New World

From the New World is a hauntingly beautiful mystery anime set in a dystopian future where psychic abilities have reshaped human society. As a group of children begins to uncover dark secrets about their seemingly utopian world, the narrative dives deep into themes of control, evolution, and morality.

With its chilling atmosphere and slow-burning suspense, this anime keeps you constantly questioning what’s real—and what’s hidden. If you’re looking for a thought-provoking story with a sinister mystery at its core, this one is a must-watch.

19. Psycho-Pass

Set in a futuristic society governed by the Sibyl System, Psycho-Pass explores the concept of justice through a cyberpunk lens. This gripping mystery anime follows Inspectors and Enforcers who must eliminate potential criminals before they commit crimes.

The deeper they dig, the more they uncover unsettling truths about the system itself. With psychological tension, philosophical depth, and thrilling investigations, Psycho-Pass is a staple for mystery and sci-fi fans alike.

18. Great Pretender

Great Pretender delivers a refreshing take on mystery through elaborate con artist schemes that span across the globe. Each arc presents a self-contained puzzle, full of unexpected twists and moral gray areas.

The vibrant animation style contrasts beautifully with the dark secrets the characters uncover. As layers peel back, you’ll find yourself hooked by its clever storytelling and charismatic cast. It’s perfect for fans who love clever mysteries with style and substance.

17. Baccano!

Chaotic, non-linear, and brilliantly woven, Baccano! is a mystery anime that keeps you guessing from the very first scene. Set during the Prohibition era in America, the story intertwines multiple timelines and characters—from gangsters and alchemists to immortals—all connected by a supernatural elixir.

Its intricate storytelling rewards careful attention, and each episode gradually unveils the larger mystery. If you love puzzle-piece narratives filled with eccentric energy, Baccano! is a wild ride worth taking.

16. Odd Taxi

On the surface, Odd Taxi may look like a quirky anime about anthropomorphic animals, but don’t let its appearance fool you. Beneath its simple facade lies one of the most intelligent and layered mystery plots in recent anime.

When a taxi driver named Odokawa gets entangled in a missing person case, secrets start to unravel across a seemingly ordinary city. Every character, conversation, and clue matters in this masterfully constructed story that delivers one twist after another.

15. Terror in Resonance

Created by Shinichiro Watanabe, Terror in Resonance tells the story of two mysterious teenagers who launch a series of bombings across Tokyo, leaving cryptic clues for authorities to decipher. But as the puzzle unfolds, their motives reveal a deeper, more tragic truth.

This mystery anime blends psychological tension with political commentary, creating a gripping narrative that forces viewers to question who the real villains are. With stunning visuals and a powerful soundtrack, it’s a short but unforgettable experience.

14. Paranoia Agent

From the mind of Satoshi Kon, Paranoia Agent is a surreal psychological mystery that explores mass hysteria and societal fear. When people across Tokyo begin to fall victim to a mysterious assailant known as Lil’ Slugger, two detectives are tasked with finding the truth behind the attacks.

But as reality blurs with delusion, the show challenges your perception of truth itself. It’s a chilling and cerebral mystery that’s as bizarre as it is brilliant.

13. The Apothecary Diaries

Set in ancient China-inspired imperial courts, The Apothecary Diaries follows Maomao, a sharp-witted apothecary who gets involved in court intrigues and medical mysteries. Using her keen intellect and scientific knowledge, she solves complex cases involving poisons, illnesses, and hidden conspiracies.

This historical mystery anime offers a refreshing mix of suspense and cultural depth, perfect for viewers who enjoy intelligent protagonists and intricate problem-solving.

12. Made in Abyss

Made in Abyss is a breathtaking mystery anime that lures you in with its charming art style—only to reveal a dark, emotional, and often horrifying descent into the unknown. As Riko and Reg journey deeper into the Abyss to find Riko’s mother, they uncover unspeakable secrets and encounter disturbing truths about the Abyss’s origin and inhabitants.

With each layer, the mystery intensifies, making it one of the most compelling and harrowing anime adventures in recent years.

11. Perfect Blue

A masterpiece of psychological horror and mystery, Perfect Blue follows Mima, a former pop idol who transitions into acting—only to be stalked and haunted by a twisted version of herself. As the line between reality and delusion blurs, viewers are thrown into a spiral of paranoia, identity crisis, and suspense.

Directed by Satoshi Kon, this anime film is a landmark in psychological storytelling and a must-watch for fans of dark, introspective mysteries.

10. The Promised Neverland

The Promised Neverland begins as a heartwarming story about children living happily in an orphanage—but it quickly turns into a chilling psychological thriller. When the kids discover the horrific truth behind their home, they must plan a daring escape while outsmarting their seemingly kind caretaker.

This mystery anime thrives on tension, mind games, and the constant threat of discovery. With clever twists and emotional stakes, it’s an unforgettable watch—especially its first season.

9. Talentless Nana

Talentless Nana is a deceptive and unpredictable mystery anime set on an island where students with superpowers are trained to protect humanity. However, the story takes a sharp turn when a new student, Nana, reveals her true mission.

Unlike traditional whodunits, this anime flips the narrative—viewers know the culprit but not how she’ll succeed… or if she’ll survive. Every episode is packed with mind games, psychological warfare, and shocking revelations.

8. Neon Genesis Evangelion

While widely known as a mecha anime, Neon Genesis Evangelion also delivers a complex and deeply psychological mystery. As teenage pilots battle monstrous beings known as Angels, darker questions arise about the true purpose of their organization, NERV, and the existential horrors lurking beneath the surface.

The anime explores trauma, identity, and human consciousness, unraveling layer after layer of symbolic and philosophical enigmas that fans are still decoding to this day.

7. Steins;Gate

Steins;Gate is one of the most critically acclaimed mystery and sci-fi anime of all time. It follows a self-proclaimed mad scientist who accidentally discovers a way to send messages through time. But with each alteration of the past, new mysteries—and consequences—begin to emerge.

The anime blends time travel with emotional storytelling and a slow-burning narrative that explodes into thrilling twists. If you enjoy stories where science meets suspense, Steins;Gate is essential viewing.

6. ERASED

In ERASED, a struggling manga artist discovers he has the ability to travel back in time to prevent tragedies. When his mother is murdered, he’s transported 18 years into the past, where he must solve the mystery of a classmate’s disappearance and stop a serial killer before it’s too late.

This emotional and suspenseful mystery anime combines time-travel drama with a powerful coming-of-age story, keeping viewers emotionally invested and constantly on edge.

5. Monogatari Series

The Monogatari Series is a unique blend of supernatural mystery, philosophical musings, and rapid-fire dialogue. Centered around Koyomi Araragi and his encounters with oddities and cursed beings, each arc presents a layered puzzle that often reflects deep emotional or psychological themes.

The series excels at subverting expectations, with visual symbolism and nonlinear storytelling that rewards attentive viewers. It’s an unconventional but brilliant experience for fans who enjoy mystery with a surreal twist.

4. Attack on Titan

At first glance, Attack on Titan seems like a straightforward action anime about humanity fighting monstrous Titans—but it quickly evolves into a dense, politically charged mystery. As the story progresses, viewers are drawn into a web of conspiracies, hidden histories, and shocking betrayals.

With every revelation, the world of Attack on Titan becomes more complex and morally gray. The series expertly builds suspense and delivers one jaw-dropping twist after another.

3. Summer Time Rendering

Summer Time Rendering is an underrated gem that blends supernatural elements with a tight, time-loop-driven mystery. When Shinpei returns to his island hometown for a funeral, he uncovers a series of bizarre and deadly events.

As he relives the same days again and again, the puzzle deepens, revealing hidden enemies and cosmic horrors. The anime balances action, suspense, and emotional storytelling, making it a must-watch for fans of mystery with a sci-fi edge.

2. Death Note

(Note: You already included ERASED at #6. Assuming entry #2 was meant to be Death Note. If that’s incorrect, let me know.)

Death Note is one of the most iconic mystery anime ever created. When high school student Light Yagami finds a notebook that allows him to kill anyone by writing their name, he sets out to create a new world free of crime. But a brilliant detective known only as “L” begins closing in. What follows is a gripping cat-and-mouse game full of deception, strategy, and moral ambiguity. With its intense psychological battles, Death Note defines the mystery genre for many anime fans.

1. Monster

Monster is the pinnacle of mystery anime storytelling. It follows Dr. Kenzo Tenma, a brilliant neurosurgeon who saves the life of a boy who later becomes a serial killer. Haunted by guilt, Tenma sets out to stop the monster he helped create, uncovering a sprawling conspiracy across Europe.

With its slow-burning tension, morally complex characters, and philosophical depth, Monster is a masterclass in suspense and psychological drama. If you’re looking for a mature, chilling, and deeply thought-provoking mystery anime, Monster is the gold standard.

Conclusion

Mystery anime has a unique way of pulling viewers into intricate worlds filled with secrets, suspense, and mind-bending twists. Whether it’s psychological thrillers like Monster and Perfect Blue, or supernatural enigmas like Steins;Gate and The Promised Neverland, each of these titles offers something unforgettable for fans who crave tension and intellectual challenge.

This list of the 20 best mystery anime showcases the diversity and depth the genre has to offer—from crime-solving dramas to existential puzzles that leave lasting impressions. No matter your taste, there’s something here that will keep you guessing until the very last frame.

So if you’re ready to dive into stories that challenge your mind and captivate your emotions, these mystery anime should be at the top of your watchlist.

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