This genre usually involves a chain of unexplained events, where the protagonist tried to solve them. Normally with an above average intellect the protagonist slowly encompasses himself in the mystery and often becomes obsessed with the case.

ACCA:13 - Territory Inspection Dept.

24 min, 12 episodes, 1 season \ seinen - mystery - police - drama - fantasy

Akudama Drive

24 min, 12 episodes, 1 season \ mystery - action - sci-fi

Another

25 min, 12 episodes, 1 season \ school - horror - mystery - supernatural - thriller - splatter

Babylon

24 min, 12 episodes, 1 season \ mystery - psychological - thriller

Baccano

25 min, 13 episodes, 1 season \ historical - action - comedy - mystery - supernatural

Bakemonogatari

24 min, 15 episodes, 1 season \ vampire - romance - mystery - supernatural

Black Butler

24 min, 46 episodes, 3 seasons \ action - mystery - comedy - historical - demons - supernatural - shounen - yaoi

Blast of Tempest

24 min, 24 episodes, 1 season \ tragedy - action - mystery - psychological - drama - magic - shounen - fantasy

BLOOD-C

24 min, 12 episodes, 1 season \ splatter - vampire - action - mystery - horror - supernatural - school

Boogiepop and Others

25 min, 18 episodes, 1 season \ mystery - psychological - horror

Boogiepop Phantom

25 min, 12 episodes, 1 season \ psychological - horror - drama - mystery - supernatural - dementia

Bungou Stray Dogs

24 min, 36 episodes, 2 seasons \ super power - action - comedy - mystery - seinen - supernatural

Case File nº221: Kabukicho

25 min, 24 episodes, 1 season \ mystery - drama - comedy

Corpse Party: Tortured Souls

30 min, 4 episodes, 1 season \ game - splatter - mystery - horror - supernatural

Danganronpa: the Animation

25 min, 37 episodes, 2 seasons \ game - crime - mystery - horror - psychological - school

Darker than Black: Gemini of the Meteor

25 min, 12 episodes, 1 season \ mystery - sci-fi - action - super power

Darwin's Game

25 min, 11 episodes, 1 season \ shounen - mystery - sci-fi - super power - action

Death Note

25 min, 1 season, 37 episodes \ psychological - mystery - police - supernatural - shounen - thriller

Death Parade

25 min, 12 episodes, 1 season \ psychological - game - mystery - drama - thriller

Denno Coil

24 min, 26 episodes, 1 season \ cyberpunk - adventure - comedy - drama - mystery - sci-fi

Erased

24 min, 12 episodes, 1 season \ psychological - mystery - supernatural - seinen

Ergo Proxy

25 min, 23 episodes, 1 season \ seinen - psychological - mystery - sci-fi - post-apocalyptic - cyberpunk

From the New World

25 min, 25 episodes, 1 season \ post-apocalyptic - drama - horror - mystery - psychological - supernatural - sci-fi

Ghost Hound

25 min, 22 episodes, 1 season \ psychological - sci-fi - mystery - supernatural

Great Pretender

24 min, 14 episodes, 1 season \ mystery - action - psychological - comedy - adventure

High-Rise Invasion

24 min, 12 episodes, 1 season \ mystery - horror - action

Higurashi: When They Cry – Gou

25 min, 24 episodes, 1 season \ psychological - dementia - supernatural - thriller - mystery - horror

Hyouka

25 min, 22 episodes, 1 season \ slice of life - mystery - school

ID: Invaded

25 min, 13 episodes, 1 season \ psychological - mystery - police - sci-fi

Ikebukuro West Gate Park

23 min, 12 episodes, 1 season \ mystery - drama

In/Spectre

25 min, 12 episodes, 1 season \ demons - mystery - supernatural - romance - shounen

Kakegurui

25 min, 24 episodes, 2 seasons \ suspense - yuri - game - mystery - psychological - drama - school - shounen - ecchi

Kemono Jihen

24 min, 12 episodes, 1 season \ demons - action - mystery - shounen - supernatural

Kizumonogatari Part 1: Tekketsu

1h 5 min, 1 episode, 1 season \ vampire - mystery - action - supernatural

Kizumonogatari Part 2: Nekketsu

1h 5 min, 1 episode, 1 season \ vampire - mystery - action - supernatural

Kizumonogatari Part 3: Reiketsu-hen

1h 23 min, 1 episode, 1 season \ vampire - mystery - action - supernatural 

K-Project

24 min, 26 episodes, 2 season \ school - action - mystery - super power - supernatural

Land of the Lustrous

24 min, 12 episodes, 1 season \ seinen - action - mystery - drama - fantasy

Made in Abyss

25 min, 13 episodes, 1 season \ mystery - sci-fi - adventure - fantasy - drama

Megazone 23

85 min, 4 episodes, 1 season \ cyberpunk - action - music - sci-fi - mystery - romance - mecha

Mirai Nikki

25 min, 26 episodes, 1 season \ splatter - action - psychological - mystery - shounen - thriller - supernatural

Mononoke

24 min, 12 episodes, 1 season \ seinen - mystery - historical - horror - demons - psychological - supernatural - fantasy

Monster

25 min, 74 episodes, 1 season \ seinen - drama - horror - mystery - police - psychological - thriller

No. 6

23 min, 11 episodes, 1 season \ post-apocalyptic - action - sci-fi - mystery - drama - shounen-ai - josei

Otherside Picnic

25 min, 12 episodes, 1 season \ mystery - shoujo-ai - fantasy - sci-fi - adventure

Owarimonogatari

24 min, 21 episodes, 3 seasons \ super power - mystery - comedy - supernatural - vampire

Pandora Hearts

25 min, 25 episodes, 1 season \ mystery - supernatural - shounen - fantasy - adventure

Paranoia Agent

25 min, 13 episodes, 1 season \ psychological - police - dementia - mystery - supernatural - drama - thriller

Pet

24 min, 13 episodes, 1 season \ seinen - psychological - mystery - supernatural

Petshop Of Horrors

22 min, 4 episodes, 1 season \ josei - mystery - horror – supernatural

Phi Brain: Puzzle of God

25 min, 75 episodes, 3 seasons \ game - action - mystery - shounen

Revolutionary Girl Utena

25 min, 39 episodes, 4 seasons \ psychological - comedy - fantasy - shoujo - mystery - drama

Serial Experiments Lain

25 min, 13 episodes, 1 season \ cyberpunk - dementia - drama - psychological - mystery - sci-fi

Shiki

25 min, 22 episodes, 1 season \ splatter - horror - mystery - supernatural - thriller - vampire

Shinsekai Yori

24 min, 25 episodes, 1 season \ psychological - drama - horror - mystery - sci-fi - supernatural

So I'm Spider, So What?

24 min, 24 episodes, 1 season \ mystery - action - magic - adventure - comedy - fantasy 

Street Fighter II: The Animated Series

24 min, 29 episodes, 1 season \ martial arts - action - mystery - adventure - shounen - drama

Terror in Resonance

25 min, 11 episodes, 1 season \ psychological - mystery - thriller

The Beginning

27 min, 12 episodes, 1 season \ police - action - mystery - psychological - supernatural - thriller

The Big O

30 min, 26 episodes, 2 seasons \ mecha - action - mystery - sci-fi - psychological

The Case Files of Jeweler Richard

25 min, 12 episodes, 1 season \ slice of life - mystery - drama

The Garden of Sinners

60 min, 7 episodes, 1 season \ mystery - action - supernatural - thriller - romance

The Melancholy of Haruhi Suzumiya

25 min, 14 episodes, 1 season \ parody - comedy - mystery - slice of life - sci-fi - school

The Millionaire Detective – Balance: UNLIMITED

24 min, 11 episodes, 1 season \ mystery - police - comedy

The Promised Neverland

25 min, 23 episodes, 2 seasons \ psychological - horror - splatter - mystery - thriller - shounen - sci-fi

The Tatami Galaxy

25 min, 11 episodes, 1 season \ psychological - mystery - comedy - romance

Tokyo Ghoul

25 min, 48 episodes, 3 seasons \ splatter - action - mystery - horror - seinen - psychological - supernatural - drama - vampire

Vampire Knight

30 min, 26 episodes, 2 seasons \ vampire - drama - mystery - romance - shoujo - supernatural

Vassalord

30 min, 1 episodes, 1 season \ yaoi - comedy - supernatural - vampire - mystery - fantasy - action

West Gate Park

24 min, 12 episodes, 1 season \ mystery - drama

When They Cry

25 min, 55 episodes, 3 seasons \ psychological - dementia - mystery - horror - supernatural - thriller

Wolf's Rain

25 min, 26 episodes, 1 season \ post-apocalyptic - action - adventure - drama - mystery - sci-fi - fantasy - furry

Yamishibai: Japanese Ghost Stories

5 min, 104 episodes, 8 seasons \ mystery - horror - supernatural - dementia - demons

.Hack//Sign

25 min, 64 episodes, 3 seasons \ isekai - game - sci-fi - adventure - mystery - magic - fantasy