Shuuichi Nitori is a 5th grade student who likes to bake and has always been something of a feminine boy. When he transfers to a new school, Shuuichi is mistaken for his 6th grade sister on his first day. Then he ends up sitting next to Yoshino Takatsuki, a tall, boyish girl who everyone calls "Takatsuki-kun." They both have secrets they can't let anyone know...
The series deals with issues such as transsexualism, gender identity, and the beginning of puberty.
Wandering Son is finished and has 15 Volumes and 123 Chapters. It is also Known as: 放浪息子, The Transient Son
Genres: School Life, Slice of Life, Drama, Romance, Gender Bender
Top 10 Manga Like Hourou Musuko [2022 List]
10. Shimanami Tasogare

After recently moving to Onomichi, Hiroshima, high school student Tasuku Kaname is thrown into despair at the possibility that he may have been outed for being gay. Convinced his life is over, his despair turns into shock when he sees a woman jump out of a window of a nearby house. Tasuku races to the house in a panic only to discover that it's a public meeting lounge owned by the woman he saw before. Tasuku comes face to face with the woman as she walks past him unharmed, but not before she implies that she had been watching him from afar. Confused, Tasuku follows her up to the top of a steep hill where she offers to briefly listen to what's on his mind. Although Tasuku doesn't go into too much detail, he later accepts her invitation to come to the lounge to meet others with similar troubles.
Our Dreams at Dusk: Shimanami Tasogare is finished and has 4 Volumes and 23 Chapters. It is also Known as: しまなみ誰そ彼, Shimanami Tasogare
9. F. Compo

Masahiko Yanagiba lost both parents and, following his mother's will, moved to his maternal uncle's family, the Wakanaes. Although Wakanaes' hospitality was heartwarming, he soon found out why his other relatives shun away from the Wakanaes: his "uncle" is a woman while his "aunt" is just the opposite. Turns out the couple took the appearance of the opposite gender, and now Masahiko has no idea whether his cute cousin, Shion Wakanae, is either a boy or a girl.
F. Compo is finished and has 14 Volumes and 102 Chapters. It is also Known as: ファミリー・コンポ, Family Compo
8. Bokura no Hentai

Three boys in junior-high who cross-dress because of differing reasons meet each other through a cross-dressing community website, and decide to meet up in real life. "Parou" started cross-dressing because he wanted to attract a heterosexual boy he liked. "Marika" is transgendered and identifies as female. Lastly, "Yui" is an antagonistic boy who adopted the persona of his older sister after her death. In contrast to Parou and Marika, Yui is sorely disappointed at the meeting.
Bokura no Hentai is finished and has 10 Volumes and 41 Chapters. It is also Known as: ぼくらのへんたい, Our Abnormalities, Our Transformations
7. IS: Otoko demo Onna demo Nai Sei

From JanimeS:
I.S. is not your everyday manga. This manga strictly deals with cases of intersexuality. I.S. stands for Inter Sexuality.
This manga deals with very serious issues with intersexuality people. The pain they go through, the troubles they confront, and ultimately their inability to reproduce and even find a partner who will accept them as they are - It's all there in a form of manga.
The series is consisted with cases, each deals with different people though some cases are much longer and more dramatic than others.
IS: Otoko demo Onna demo Nai Sei is finished and has 17 Volumes and 79 Chapters. It is also Known as: IS ~男でも女でもない性~, I.S., IS, Intersexuality, Inter Sexuality, Aiesu
6. Ao no Flag

The "youth pure love" story begins when three students in their third and final year of high school meet during a time when they are worried about paths for their futures. Waiting for them are sweet, painful, and heartrending days.
Blue Flag is finished and has 8 Volumes and 54 Chapters. It is also Known as: 青のフラッグ, Blue Flag
5. Hikari to Tomo ni...: Jiheishouji wo Kakaete

Born during the sunrise—an auspicious beginning—the Azumas' newborn son is named Hikaru, which means "light." But during one play date, his mother notices that her son is slightly different from the other children. In this alternately heartwarming and bittersweet tale, a young mother tries to cope with both the overwhelming discovery of her child's autism and the trials of raising him while keeping her family together. This is a story that resonates not only for those whose families have been affected by autism, but also for all past, present, and future parents.
Included one-shots:
Volume 15: Thank You Sensei!, Haru no Manazashi
With the Light: Raising an Autistic Child is finished and has 15 Volumes and 92 Chapters. It is also Known as: 光とともに… ~自閉症児を抱えて~, Thank You Sensei!, Haru no Manazashi
4. Houkago Hokenshitsu

Like most teenagers, Mashiro Ichijo has a secret. But Mashiro’s secret is that he’s neither fully male nor female! So far, Mashiro’s been able to live his life as a boy, but all this changes when he’s informed of a new class he must take in order to graduate from his elite prep school. To pass, he must find the “Key”…and the only way to find it is to enter into a nightmare world where his body and soul are put at the mercy of the worst kind of enemies: his classmates!
After School Nightmare is finished and has 10 Volumes and 39 Chapters. It is also Known as: 放課後保健室, Afterschool Nightmare
3. Shishunki Bitter Change

Yuuta and Yui had their body swapped when Yuuta fell down from a tree. How will they co-operate dealing with this as they grow up?
Shishunki Bitter Change is finished and has 0 Volumes and 65 Chapters. It is also Known as: 思春期ビターチェンジ, Shisyunki Bitter Change
2. Oyasumi Punpun

Punpun is an ordinary young boy growing up in Japan whose age of innocence has reached its end after his father is arrested for spousal abuse and putting his mother in the hospital. With his uncle looking after him, Punpun grows into adulthood facing a series of events which change him, for better or worse, forcing him to contemplate just what it means to be an adult.
Goodnight Punpun is finished and has 13 Volumes and 147 Chapters. It is also Known as: おやすみプンプン, Dobranoc, Punpunie, Bonne nuit Punpun!, Boa noite, Punpun, Bona nit, Punpun, Buenas noches, Punpun, Gute Nacht, Punpun, 잘자 뿡뿡, 晚安布布, לילה טוב, פונפון, Buonanotte, Punpun, İyi Geceler, Punpun, ฝันดีนะปุนปุน
1. Shounen Note

A short story about a boy whose name is Yutaka and sucessfully sings as a soloist in a choir with his soprano voice, but then gets into the trouble of his puberty vocal change.
A serialized version of the oneshot Octave.
少年ノート is finished and has 8 Volumes and 40 Chapters. It is also Known as: 少年ノート, Octave, Days of Evanescence, Octave, Days of Evanescence