15 Anime Movies With Mystery

Anime movies with mystery are truly a godsend. They are significantly shorter than the mystery anime series but still achieve the same effect. It only takes you about an hour and a half to watch one, and you still get to forget how boring and uneventful your own life is. And if you by any chance manage to solve part of the puzzle on your own, you get to feel smart!

For these reasons, I decided to gift you a list of mystery anime. Not just any anime movies with mystery, but what I believe to be the best ones. Even with all the perks that come with the genre, a bad mystery is not appealing to watch. We all want grand plot twists, good action, a showcase of genius detectives and criminals, and of course, a satisfying conclusion. 

The movies on the list have it all! They’ll keep your attention, immerse you in the story, and make you question what is real. So sit back, relax, and prepare to watch the 15 best anime movies with mystery!

Top 15 Anime Movies With Mystery That Will Blow Your Mind


  • The list consists of the best anime movies with mystery that will keep you on edge the whole time
  • The ranking, as always, is based on personal preference
  • The list is diverse, to say the least… there is everything from coming-of-age and romance anime movies with mystery to mecha and psychological thrillers

15. Lonely Castle in the Mirror

Anime Movies With Mystery: Lonely Castle in the Mirror

What’s a better way to start the list than with the mystery anime that will call you out on your non-existent social life? Don’t worry, it won’t be the sole focus of the film, but it’s relatability will immerse you in the story.  

In a quiet neighborhood in Tokyo, seven students avoid school like a plague. They lock themselves in their rooms, hiding from all social interaction (honestly, same). Their isolation lasts until the mirrors in their rooms start to shine.

One touch takes them to a beautiful castle, saving them from a lonely life. Although it is their playground and safe space during school hours, this is not paradise. There is a key hidden in the castle that can grant one wish, but there is a catch!

They have to find the key by the end of the school year, and they have to leave the castle every day before five o’clock, or they will meet a fatal end.

It would be nice to escape the loneliness of this life by simply touching the mirror… However, while we don’t have access to such power, the ability to watch these anime movies with mystery will help us push through!

14. Penguin Highway

Anime Movies With Mystery: Penguin Highway

One important aspect of anime movies with mystery is solving important cases. Sometimes it’s robberies, sometimes murders, and sometimes it’s penguins!

Aoyama is a very smart boy whose intelligence can be compared to that of adults. However, this does not prevent him from developing a crush on a nice woman he met at the dentist’s office.

One morning, penguins start appearing in his neighborhood. Aoyama is determined to find out what’s behind this and joins forces with his crush to uncover the secret of penguins!

This anime mystery has it all: the case that will keep you interested, entertaining characters, and most importantly, cute animals! If you are ready for a fun adventure with sci-fi elements, give Penguin Highway a shot. And please, don’t let annoying kids discourage you!

13. The Case of Hana & Alice

Anime Movies With Mystery: The Case of Hana & Alice

Murder mysteries are the core of this genre. Therefore, it’s impossible to make a list of the best anime movies with mystery without one.

A new environment, bullying at school, and an overbearing mother make Alice’s life much more difficult. That’s why she turns to important things like solving a murder. One of the reasons others mistreat her, besides being idiots, is because she sits at a table that belonged to “Judas“.

Alice wants to unravel the mystery of his murder, and the clues lead her to Hana, who agrees to help her.

You have to respect Alice for her determination. The girl really said, “People are boring so I’m just going to investigate a murder.” Shout out to Hana as well. It takes courage to just be on board with the crazy idea of a person you don’t know.

12. UN-GO: Chapter of Inga

UN-GO: Chapter of Inga

If you’re looking for great detective mystery anime, always check if your favorite series in this genre has a movie. And if it does, 9 times out of 10, you hit a jackpot! One such example is Un-Go, which I recommend with my whole heart! However, you might want to watch the film first.

This prequel takes place at the same time as the first episode of the series. We are introduced to new mysteries and discover the story of the main duo.

Don’t let Un-Go stay one of the most underrated anime movies with mystery!

11. Professor Layton and the Eternal Diva

Professor Layton and the Eternal Diva

Of course, while movies within a franchise are mostly a go-to for mystery anime fans, stand-alone films can do just as well. At least that’s the case with Professor Layton and the Eternal Diva.

Professor Hershel Layton is a versatile personality – an archaeologist, a puzzle solver, and an extraordinary gentleman. One day, he and his apprentice Luke Triton receive a mysterious letter from his former student Janice Quatlane.

The letter contains tickets for the opera Crown Petone, which turns out to be far from a normal show. It is a game and the main prize is the Fountain of Youth which can give eternal life. However, this is only the surface of a larger mystery that this team must unravel.

Now the truth is that I gave the film a chance because of its unique art style. Nevertheless, it turned out to be one of the most entertaining anime movies with mystery. I was literally glued to the screen for almost two hours and let me tell you: I would do it again!

10. The Tunnel to Summer, the Exit of Goodbyes

The Tunnel to Summer, the Exit of Goodbyes

Now… Why watch regular mysterious anime when you can watch romance anime movies with mystery? I am sure that I am not the only one who believes that a sprinkle of romance makes everything more interesting. In the case of The Tunnel to Summer, the Exit of Goodbyes, this is one hundred percent true.

School student Kaoru Touno‘s life is in chaos. After the death of his sibling and the divorce of his parents, he gets into a fight with his father and runs from home. That’s how he reaches a mysterious tunnel that pulls him inside. Terrified by what he sees there, he tries to escape and along the way picks up a bird that looks like his dead pet.

Kaoru manages to get out but realizes that even though he spent a few minutes in the tunnel, a whole week has passed outside. Everything gets more complicated when he realizes that he was followed by a new transfer student, Anzu Hanashiro. She asks him to help her in the experiment and find out if the so-called “Urashima Tunnel” really grants wishes.

The only problem with this movie is that you won’t be able to follow the mystery properly because the beautiful scenery and amazing animation will distract you. Interesting, beautiful, and romantic… What else can you ask for?!

9. Death Billiards

Death Billiards

I’ll just assume all of you have watched Death Parade because I refuse to accept that there is someone who hasn’t. If by any chance you are that person, it’s fine! That just means you get to experience this masterpiece for the first time. And for all of you who mourned the ending of the show, here is one of the best anime movies with mystery!

Very similar to the anime series, the story is set in Quindecim. Two men are new guests of a bar where an arbitrator is waiting for them. Namely, the two of them will have to play a game randomly selected by roulette, and if they refuse, they will face severe consequences.

They are to play it as if their life depended on it. The game that will decide their fate is billiards, and this time it’s much more than just getting balls into holes.

8. Bungo Stray Dogs: Dead Apple

Bungo Stray Dogs: Dead Apple

It’s kind of given that anime whose main characters are detectives will be one of the best anime movies with mystery. Bungo Stray Dogs is one of those shows that will surprise you no matter what. It doesn’t matter how hard you try to follow everything, you won’t be able to solve the case. 

It is a hard hit on the ego, but the anime is so addicting that you’ll keep trying and getting surprised till the end. The movie Dead Apple is the same!

A great disaster has befallen the Earth, and the detective agency has once again found itself at the center of events. After the appearance of the mysterious fog, the users of the ability began to commit suicide one after another. The clues lead our detectives to “Collector“, a mysterious man of unknown abilities, who may be the mastermind behind everything.

7. Lupin III: The First

Lupin III: The First

Quickly! What do we get when we combine great anime movies with mystery and the best action anime? Answer: One of the most legendary franchises in the world of animation! Lupin the Third is everything a fan of mystery crime anime movies could ask for.

The best thing is there is so much content that you’ll never run out, and I highly recommend you start this journey with Lupin III: The First.

Everyone’s favorite “gentleman thief” Lupine III jumps into another action-packed adventure! This time, the colorful crew’s goal is to uncover the secret of the Bresson Diary before it falls into the wrong hands. Various enemies, creative traps, and other dangers will await them, but nothing will prevent Lupine the Third from solving this case as well.

6. The Disappearance of Haruhi Suzumiya

The Disappearance of Haruhi Suzumiya

The Melancholy of Haruhi Suzumiya was one of the best mystery anime of its time. So it’s no surprise that the sequel is one of the best anime movies with mystery. Maybe I am biased as this is one of the shows I love a little too much, but I firmly believe you can’t go wrong with this anime. It’s simply too fun, entertaining, and well-written. Like that MyAnimeList score of 8.60 is no joke…

The protagonists of the story are once again members of the SOS Brigade. However, nothing is as it was except for Kyon who has to deal with these changes.

When he comes to school one day, he finds out that Haruhi Suzumiya and Itsuki Koizumi are missing, Mikuru Asahina doesn’t recognize him, Yuki Nagato is an ordinary person, and Ryouko Asakura is back. This puts Kyon in front of a choice: to continue living the normal life he’s always longed for, or to solve this mystery.

5. xxxHOLiC The Movie: A Midsummer Night’s Dream

xxxHOLiC The Movie: A Midsummer Night's Dream

xxxHOLiC The Movie: A Midsummer Night’s Dream is the definition of mysterious anime. The reason for that is the fact that the genre itself is the least mysterious part of it. The real mystery is how someone thought to write such a bizarre story and then animate it. Why is the name so freaking long? And more importantly, why is something this goofy and weird actually so good?

While his peers are on summer vacation, Kimihiro Watanuki continues to work as an assistant to the lazy Yuuko at her shop. However, his peace does not last long as a new paranormal situation reappears.

Yuuko gets an invitation to a mysterious mansion whose owner wants her powers. Together with Watanuki’s schoolmate Shizuka Doumeki,  they go to see what’s going on. It seems that they are not the only ones invited and a large number of collectors are there as well. However, they start disappearing one by one and now it’s up to this trio to find out what’s going on.

Don’t let the unusual animation and art style turn you away from one of the best anime movies with mystery. It’s strange, but that’s the charm!

4. When Marnie Was There

When Marnie Was There

It’s Studio Ghibli time! Among many outstanding films from this legendary studio, one that definitely stands as the best mystery anime is When Marnie Was There. 

Anna Sasaki is a sickly child whose constant asthma attacks have forced her parents to send her to the countryside. There, she discovers an abandoned mansion, and in it a little girl, Marnie. Although her origin is a mystery, that doesn’t stop Anna from befriending her. However, the ball of mystery slowly begins to unfold and it becomes clear that Marnie is not an ordinary girl.

Spoiler alert: You won’t solve the mystery. You can try, but I guarantee you it will shock you.

3. Case Closed Movie 06: The Phantom of Baker Street

Case Closed Movie 06: The Phantom of Baker Street

You didn’t think that the list of detective mystery anime would go without the most famous detective in the anime world, did you? Detective Conan is a must when it comes to the best mystery anime and you know it!

So it wasn’t a question if it would make the appearance, but which movie you should watch first? As this is the list of best anime movies with mystery, you need to give Case Closed Movie 06: The Phantom of Baker Street a chance!

Noah’s Ark is the latest VR innovation to be presented to the privileged children of Japan. This event, however, is disrupted by the murder of one of the employees who left the last message on Ark.

Conan Edogawa and his gang try to solve this case. However, upon entering the Ark, the machine gains its will and locks both them and the children away. Now, in order to escape and solve the case, they must go through 19th-century London and track down the famous Jack the Ripper.

2. Ghost in the Shell

Ghost in the Shell

Ghost in the Shell is one of those anime movies that if you watch people will assume that you are elitist… And it’s worth it! Sure, someone will accuse you of thinking that you are better than anyone but guess what? You are! You survived one of the top-tier detective anime movies!

The year is 2029 and the world has reached a completely new level of technological development. Major advances in cybernetics have allowed people to replace their body parts with robotic ones, making humans and machines more connected than ever. With great progress comes new problems and Public Security Section 9 is here to fight them.

Major Motoko Kusanagi has taken on a new case involving the mysterious hacker “Puppet Master” who leaves his victims with no memories. As Motoko and her team follow the trial of this criminal, it becomes clear that the case is much more complex than it appears. This prompts the ambitious detective to question her own existence.

Oh.. Did I mention that this movie will break you and your sense of identity? Well, it’s one of the things that makes it one of the best anime movies with mystery!

1. Paprika


Among the best anime movies with mystery, there is one that has to be crowned as the best of the best. Today, after many considerations, it’s Paprika!

The dream world is still a mystical place, but it definitely gives a unique insight into the human psyche. That’s why a tech lab started developing the “DC Mini“, a device that allows us to enter the dreams of others. Atsuko Chiba and Kosaku Tokita are doing their best to use this technology to explore the thoughts of their patients and thus cure them of their psychological problems.

However, this is a dangerous device and if it falls into the wrong hands, it could be used for psychological terrorism. So when “DC Mini” goes missing and people around them start acting strangely, Atsuko and Kosaku know they have to do something. They seek help from Officer Konakawa, who has experienced their experimental treatment and set off on a search.

The story literally takes place in the world of dreams – the most mysterious place known to humans! This, combined with the genius directing of Satoshi Kon, makes a mystery anime that will, almost literally, blow your mind. And if that doesn’t make it the best anime movie with mystery, I don’t know what does!

Final Notes:

This list proves two things. First: people are ready to make up the craziest stories ever just to forget their loneliness and feel smart. Second: We need more stand-alone mystery anime movies!

In any case, each of these films is worthy of attention and will not leave you indifferent. And if that’s the case, I suggest you check out our other movie recommendations!

Frequently Asked Questions:

1. What are some good mystery anime series?

Mystery is quite a popular genre, so there are many great shows to watch. Some of the most popular ones are Death Note, Monster, Steins;Gate, Erased, and Psycho-Pass.

2. Where to watch these anime movies?

All of these movies are available on either Crunchyroll or Netflix.

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