The 50 Best Mystery Anime of All Time, Ranked (2026)
Last updated: 2026-05-03 · Entries are ranked by MyAnimeList community score, pulled once and cached so the list stays stable between manual refreshes. Each season is treated as its own entry, matching MAL's catalog. Top-10 blurbs are written by the Anime Facts 101 team and reflect editorial perspective, not raw score order. Last refreshed 2026-05-03. Score data sourced from MyAnimeList community ratings via the Jikan API.
Mystery anime operates on a contract with the audience: here is a puzzle, and we promise the answer will be worth following. What separates a satisfying mystery from a frustrating one is fair play — whether the information needed to understand the solution was available, even if not obvious. The best mystery anime are the ones you can rewatch and find the seams of the answer hidden in plain sight.
The genre spans true detective procedurals, supernatural investigations, historical whodunits, and conspiracy thrillers — and the best entries commit to their premise without cheating. When the mystery resolves, it should feel inevitable and surprising at the same time. That combination is harder to achieve than it sounds, which is why the shows that do it consistently tend to sit at the top of any community ranking.
This list is ranked by MyAnimeList community score across every mystery-tagged anime on the site, with editorial blurbs on the top 10 explaining why each one earns its spot. Seasons and films are treated separately.
- 1
Steel Ball Run: JoJo's Bizarre Adventure
2026 · ? eps · Score: 9.15
Steel Ball Run tops this list at 9.15, which might surprise viewers who think of JoJo as an action franchise first. But Steel Ball Run is genuinely a mystery at its core — the race is a cover for a search for holy relics, Valentine's plan is revealed incrementally, and the show parcels its revelations with care. The mystery of what the Steel Ball Run actually is drives the story from start to finish.
- 2
The Apothecary Diaries Season 2
2025 · 24 eps · Score: 8.91
Apothecary Diaries Season 2 earns 8.91 as the continuation of one of the genre's most consistent procedurals. Maomao's medical knowledge is the lens through which she solves palace intrigues, and Season 2 expands the political scope while keeping her analytical voice sharp. The mystery engine never stalls even as the cast grows larger.
- 3
Monster
2004 · 74 eps · Score: 8.89
Monster scores 8.89 across 74 episodes as an anime that treats its central mystery — the nature and history of Johan Liebert — as a philosophical question as much as a plot one. Dr. Tenma's chase across post-reunification Europe is dense with secondary mysteries, and the show trusts its audience to hold a lot of threads at once. It's the most literary mystery anime ever made.
- 4
Owarimonogatari Second Season
2017 · 7 eps · Score: 8.86
Owarimonogatari Second Season earns 8.86 as the Monogatari entry where the series' accumulated mysteries come to a head. Araragi's past and the origins of his relationship with Oshino Meme are finally addressed directly, and the answers are stranger and more satisfying than a less ambitious show would risk. The mystery payoff here is the best the franchise has produced.
- 5
The Apothecary Diaries
2023 · 24 eps · Score: 8.85
The original Apothecary Diaries (8.85) establishes Maomao as one of the genre's best protagonists — a pharmacist in an imperial court who can't stop herself from investigating things that aren't her business. Each case connects to the larger political world around it, and the show respects the audience enough not to explain the answer before Maomao gets there.
- 6
Kizumonogatari Part 3: Cold-Blooded
2017 · 1 ep · Score: 8.78
Kizumonogatari Part 3 scores 8.78 as the conclusion to the Araragi origin trilogy that explains what kind of vampire he is and what it cost him to become it. As a mystery, it's unusually direct for the Monogatari franchise — less verbal sparring, more revelation — and the answers it provides recontextualize everything in the main series.
- 7
Monogatari Series: Second Season
2013 · 26 eps · Score: 8.76
Monogatari Series: Second Season (8.76) is where the franchise's mystery structure fully reveals itself — multiple arcs with separate supernatural cases that turn out to be related in ways that become clear only in retrospect. Mayoi Jiangshi and Shinobu Time are particularly strong as self-contained mystery stories.
- 8
Mushi-shi: Next Passage Part 2
2014 · 10 eps · Score: 8.72
Mushi-shi: Next Passage Part 2 earns 8.72 as mystery in a quieter register — each episode a standalone case where Ginko investigates a mushi causing strange phenomena in rural Japan. The mystery is often about understanding rather than solving: what is this creature, why is it here, what do people have to do to live alongside it? The gentleness of the format is itself part of the genre.
- 9
Mushi-shi: Next Passage Part 1
2014 · 10 eps · Score: 8.69
Mushi-shi: Next Passage Part 1 (8.69) continues the same gentle anthology mystery format. Each episode is its own complete mystery with its own resolution, and the show's willingness to let some cases end badly rather than neatly is what keeps it honest. Ginko is one of anime's best observer-protagonists.
- 10
Link Click
2021 · 11 eps · Score: 8.69
Link Click earns 8.69 as a Chinese anime that combines time-travel mechanics with emotional mystery in a way that earns genuine comparison to the best Japanese entries in the genre. The photo-travel premise is used with increasing sophistication, and the friendship between Cheng Xiaoshi and Lu Guang becomes the emotional anchor for a conspiracy that grows darker each arc.
