8 Best Isekai Anime With Mystery Elements (2024)

Tired of watching the same tropes in Isekai Anime? Well, we might have the right thing for those who have been seeing the same story (and the same kind of main characters) doing the same things over and over. These Isekai series combine Mystery Elements in such a seamless way that the story becomes quite intense, and the plot twists are guaranteed to blow viewers' mind.

Fans might never heard of these titles before, or perhaps haven't had a chance to watch them yet. So, this list will guide them through everything they should know about the best Isekai Anime that blends Mystery in their plot, and why they are worth watching.

8 The Vision Of Escaflowne

The Identity Of The Main Villain Will Blow Your Mind

The Vision Of Escaflowne was perfect in every sense: it had all the right ingredients of a very successful, yet highly underrated anime. It had romance, mystery, conspiracies, and a villain who in all lights looked like the typical egotistical tyrant until he revealed his true identity and blew fans' heads with one of the biggest revelations in anime history.

If fans are looking for an anime where Giant Mechas fight against Dragons, to steal their hearts and power up themselves, and where a school girl ends up in the middle of a wide-scale fantasy war, then look no further. This is the series they need.

7 My Instant Death Ability Is So Overpowered

Watch It Again, And You Might Discover A Dark Hidden Mystery

Fans might have watched this already and said: okay, this is yet another Isekai Anime with an Overpowered main character. But, as time went by, I decided to give it another chance, and discovered an incredible detail about Yogiri Takatou's true identity. It was so well hidden, and lying there in plain sight that nobody thought about it. Why nobody can say Takatou's true name?

Delving deeper into this mystery, and confirming the suspicions by reading the Light Novel, I can say that it is truly a well-hidden secret. So, if there's another season of this show, things might get fascinating for Takatou and his faithful companion Tomochika.

6 The Twelve Kingdoms

One Of The Few Isekai's Based On Asian Folklore

Another underrated Isekai Anime from the early 2000s that dived head-on into the Asian Myths of Kunlun, with a mix of the Warring Kingdoms, and Journey to the East. From minute one we can perceive this anime is different than most, and it's not pure nostalgia talking here: the animations, designs, and character developments are simply too good. But what drives the engine of this incredible story, is the Mystery of the Kirins and the Monarchs.

Since the anime didn't cover many of the hidden secrets of the Light Novels (and there are quite a few) most fans of the series have been craving to see a new adaptation of this incredible anime. But the studios that produced it are way too busy producing Bleach to give this anime a fair chance. What a waste of potential.

5 The Faraway Paladin

One Of The Few Isekai Anime Where The Main Character Doesn't Remember His Past Life

I found this anime series by following the Manga, which was relatively unknown for some reason. This Isekai is one of the best I've seen, and it hides a mystery that will make a few fans of Fantasy's gears grind for the years to come. In the first place, the main character speaks Elven, and not any random version of this fictional language, but the Tolkien version of it. Yes, that's right, from The Lord Of The Rings, The Silmarillion, and The Hobbit.

And if that wasn't the only strange cameo, then some of the Gods in the series suspiciously resemble the Valar of Tolkien's tales. More so, there seems to be a mixture of certain events that could be related to various Tolkien stories. So, was The Faraway Paladin inspired by the father of modern fantasy, or is there something else? Fans will have to watch and see for themselves what lies hidden in plain sight.

4 Not Allowed In Another World

If Tim Burton Made An Isekai, It Would Be This One

Not Allowed In Another World is one of those Isekai that greatly surprises fans once they give it a chance. With a strange and gloomy main character, who is so self-destructive that it hurts to watch, and constantly talks about how beautiful it would be to die, it is hard to see beyond this gloomy vibe. But overcome that initial shock, and there's the perfect Satirical Isekai Anime right there, ripe for the taking, and with some great character developments to boot.

And it also has one of the strangest and most mind-breaking mysteries to solve in all Isekai anime: who is the true villain of the story. At first, it seems like the "otherworlders" that were drawn to this fantasy world and constantly abuse their powers are the enemy. Then, it becomes less obvious by the second, just to redirect the audience's attention with a suckerpunch that nobody expected. But well, there's a new season incoming, so we will have to wait and see how the mystery unfolds.

3 Tsukimichi: Moonlith Fantasy

The Greatest Mystery Of All: When Will The MC's Mind Finally Break?

Makoto Misumi is one hell of a main character, and his development throughout the series has proven to be quite atypical for the average OP Isekai protagonist. So, who is Makoto, really? Those who have read the Light Novels are far ahead of those watching the series in solving this mystery. But that's not the only riddle to solve in the series, and fans will have a great deal of mind-boggling conundrums in this great fantasy tale, including a crazy theory that links this series' main villain with that of Failure Frame.

But perhaps the greatest mystery of them all is: when will Makoto finally snap and burn everything apart? With all things considered, he has seen his fair share of suffering, and had a couple mental breakdowns, but he seems to always come back to his senses. He seems to be way too grounded to become a cliché edge lord, so we need to wait and see where this goes. One thing is for sure: it will be worth the wait.

2 The Eminence In Shadow

Shadow's True Identity And The Secret Behind His Incredible Magic

Many fans of the Isekai genre might look at The Eminence in Shadow and see just another overpowering MC who pretends to be an edge lord, but it is truly delusional and suffers from a severe case of 8th grader syndrome. But the charm of this show doesn't lie in the flashy action scenes, nor in the sharply dressed female characters, and even less in the main plot. It lies in the sub-stratus of the plot, that it's actually a huge puzzle to be solved by the fans.

Where is Shadow living right now? Is it another world, or is this a Dystopian future Earth where magic was brought due to a supernatural phenomenon that reshaped reality? Was it the same phenomenon that dragged Cid toward the Fantasy World? Or was Cid, in a complex paradox-like plot twist who brought the magic to Earth by dying and becoming Atomic for the first time? There are a lot of theories about what's really going on behind all the smoke and mirrors of the series and its ridiculous characters. What's undeniable, is that this is one of the most well produced anime series of the genre, and is definitely worth watching.

1 Wise Man's Grandchild

Has One Of The Best Villains Of Isekai Anime, And One Of The Best Mysteries As Well

In this Anime, Shin Wolford is a talented magician who got reincarnated in a fantasy world and was raised by two of the greatest magicians in the world. So far, the average Isekai MC background. But later, it becomes evident that this series is not as simple as it seems at first. For starters, the protagonist avoids the harem route and settles down with a single marriage partner (Cecily). Then we get to know one of the best Villains of the genre: Oliver Schtrom, with a past so tragic and an origin story so complex and mysterious that can by itself sustain the plot.

Why do humans become demons and try to destroy the world? Has this always been this way, are all mages destined to become demons if they lose control of their emotions, or is there another mysterious factor involved, hidden in the shadows? We might have to wait until season 2 to find out, but in the meantime, there are a lot of Manga episodes to read and fill the void.