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A girl wakes up to find her room a mess. She realizes that she has partially lost her memory. All she can remember is that her name is Maze, and that she's now in a strange world. Her house landed on some creatures just like Dorothy in The Wizard of Oz. Where she meets a girl named Princess Mill who is on the run from the "Jaina Holy Group"; Maze also soon realizes that at night she transforms into a man. Maze and Mill meet more companions on their journey and become embroiled in a war to defeat Jaina and raise Mill back to the throne of Bartonia. (Source: MU)

A sequel roughly translated as Divine Melody: Chapter of Warm Snow is currently serialized in Star Girls. It follows the adventures of Cai Sheng during the last chapter of Divine Melody. (Source: Wikipedia)

The romantic comedy story centers on Saku Tsukimiya, a male high school student who is as beautiful as a girl. On the night of his 17th birthday he has a dream wherein a mysterious voice refers to him a princess. When he wakes, a mysterious being tells him that he is the reincarnation of Princess Kaguya, and his body has undergone a transformation. (Source: Akita Shoten, translated)

Rintaro and Haruto are two friends who enjoy playing the VRMMO Eternal Maze Online, a fantasy video game where you can be a different person from the real world and enjoy a second life. One day Rintaro finds a mysterious item called the Reincarnation Jewel in his inventory so he decides to use it and teleports himself and his friend to a fantasy world. Rintaro became his female avatar who is a magician and Haruto his male avatar a strong paladin. Both stunned by what happened, they will search for information on how to get out of this fantasy world while at the same time trying to survive in this strange world so that they can return to their normal life. (Source: Takeshobo, translated)

A humorous short about a boy who transforms into a girl to save the world. (Source: M-U)

Despondent that the girl he loves does not return his affections, Eitaro attempts to commit suicide. But his near dead-body is discovered by a scientist and his mind is transferred to the body of a young girl. As a girl, Eitaro soon lears that the girl of his dreams did in fact love him, so they try to make the relationship work despite the fact that Eitaro is in a girl's body. Source: ANN

In this all-boy school, the "Girl Day" is the event on which some of the boys become girls, only returning to their original bodies after a few days. Their duty: to tame the other boys by compensating the absence of female students with their own feminine body.

The story is set in a high school "Idol Club." Mitsuki Tsunoda, an idol otaku high school boy, suddenly becomes a girl—but only physically. Soon after, his favorite former idol, who once disappeared from the spotlight, appears right before him! Aiming for the top with your favorite idol! A gender-bender school idol comedy begins! (Source: MANGA Plus)

Ren Yoruno is an ordinary high school boy whose hobby is writing web novels. However, he finds that due to his lack of interactions with the opposite sex, he has no idea how to write female characters. That's when he finds an ad about a miracle drug that can make you understand the feelings of women. But when he drinks it... (Source: Kadokawa, translated)

Tohru and Noburo are brothers of the Takagami Family. Toru has Yin in his blood and is constantly targeted by the youkai and other creatures lurking in Japan. When Tohru is targeted by one, his brother Noburo releases the fox deity Kuugen Tenko who protects Tohru from the monster. Kuugen now acts as the protector of Tohru and Noburo to keep them safe from any threats to them, while at the same time trying to adapt to the modern world. (Source: Wikipedia)

Liz, who can see the future, has her engagement broken off because of her mysterious power. That sort of woman has been hired as a maid by Her Highness Queen Schriess of Lynphilia. Around Her Highness, who has never married and has no heir, her five younger brothers, the princes, have started a struggle for succession. However, Liz learns that the queen, who must urgently marry for the sake of national peace, has a big secret!? (Source: Kodansha, translated)

A collection of stories about Hikaru Anjou, a guy who suddenly became a girl.

Yuuri Onagawa is a young boy about to enter high school, who constantly pines over his childhood friend Kyouko. One day he meets her after years of separation, only to find out that she despises men now. Upset, he prays at a shrine to have them become friends once again. The god fulfills his wish, but in a way he never expected... (Source: MU)

One morning detective Akira Tachibana wakes up to find that he has changed into a woman without knowing why, She decides to keep doing detective work and continue to take cases until she finds more clues to solving the mystery of why he became a woman. Included one-shots: Volume 2: Dai-07 Shoutai, Dai-07 Shoutai: Black ver.

XXXX, a man used and abused for general tasks by his adventuring party, finds himself on the verge of death in dragon territory in the Kugus Mountains after a party member stabs him in the back. Literally. Next time he opens his eyes, he's in the nest of a red dragon named Kaphal whose egg was destroyed in a natural disaster. Having lost both his memories and his name, he turns instead into a young girl named Lushera. And apparently Kaphal plans to raise Lushera as her own daughter...? This is the story of the odd fate binding one dragon and one human, the story of an unconventional mother and daughter. (Source: Cross Infinite World)

This is a spin-off of the series Night Wizard. It has completely different characters. Ryuunosuke changes into a female wizard when he senses monsters called Emulators. (Source: MU)

Souji Mitsuka is an ordinary high school boy who has an obsession for twintails. One day he encounters a mysterious girl named Twoearle, who is from a parallel world, when monsters appear in his town and declare that all twintails in the world belong to them. These monsters feed off "attribute strength," the spiritual energy of humans. Twoearle entrusted Souji with Tail Gear, imaginary armor initiated by powerful twintail attributes. With the armor, Souji transforms into a girl and twintail warrior branded Tail Red, to protect Earth. (Source: MangaDex)

The story follows the high school student Jintarou Futsu, whose confession was rejected by his crush. His misfortune continues, as news of a gender-change disease turns Jintarou into a beautiful silver haired girl. The shock of it causes him to try to escape from reality by playing the VRMMO, Clan/Clan... His game character uses the same girl appearance as in real life, and the Alchemy skill, which most players call a trash skill. He meets lots of fellow adventurers, and becomes stronger within the game world of Clan/Clan's slogan, "When one becomes an adventurer, they can fight, steal, control, explore, invent, create, and do anything as they like." He meets a wide variety of adventurers that help him grow, while hiding what happened to his appearance as a bug to his friends who also play the game, and hides the fact that he had become a girl in real life. When summer break is over, he will have to show his face at school. This is about one of the best National-class adventurers, the story of the Alchemist who won a war without even taking a single step. When a normal high school student suddenly turns into a beautiful girl, what would they do? The answer is to that is to become a net-game addict! (Source: Shousetsuka ni Narou, translated)

Yuri is frustrated that her childhood friend, Taku, is not very masculine. She wants to level-up their relationship but Taku just can't make any bold or sexual advances. Then one day an evil spirit (youma) pops in on Taku and tells him about a prophecy foretelling of a time when Taku's offspring will save the world. After finishing the tale, the youma immediately puts a curse on Taku's balls in order to stop the prophecy from coming true. But that curse has made Taku more feminine than ever. Is Yuri's dreams of a love-love relationship with Taku over, or can she help Taku find his masculinity? (Source: MU)