11-nin Iru!
11人いる! (1975)

Drama, mystery, sci-fi, shoujo
Intersex protagonist

Licensed as They Were Eleven! by VIZ Media and Denpa.

Shiawase Enikki
しあわせ絵日記 (1996-2002)

Comedy, slice of life, josei
Has a bi character

Currently not licensed.

Kakumei no Hi
革命の日 (1999)

Comedy, school life, shoujo
Intersex protagonist

Licensed as The Day of Revolution by Digital Manga Publishing.

IS: Otoko demo Onna demo Nai Sei
IS ～男でも女でもない性～ (2003-09)

Drama, school life, josei
Intersex protagonists
Recommended

Currently not licensed.

Honey & Honey: Onnanoko Doushi no Love Couple
ハニー＆ハニー 女の子どうしのラブ・カップル (2006-2007)

Comedy, drama, slice of life
Has a bi character
Autobiography

Currently not licensed.

Ohana Holoholo
オハナホロホロ (2008-13)

Drama, slice of life
Has a bi character

Currently not licensed.

Seibetsu nante Kimerarenai!
性別なんて決められない！(2011-12)

Slice of life, josei
Intersex protagonist
Autobiography

Currently not licensed.

Mangosteen no Koibito
マンゴスチンの恋人 (2013)

Drama, school life, shoujo
Has an intersex character

Currently not licensed.

Kiryuu-sensei wa Renai ga Wakaranai.
桐生先生は恋愛がわからない。(2015-17)

Comedy, josei
Aro/ace protagonist

Currently not licensed.

Shimanami Tasogare
しまなみ誰そ彼 (2015-18)

Drama, school life, coming out, seinen
Widely acclaimed work, featuring many different identities across the LGBTQ+
Has an aro/ace character
Written by an x-gender author
Recommended

Licensed as Our Dreams at Dusk: Shimanami Tasogare by Seven Seas Entertainment.

Yagate Kimi ni Naru
やがて君になる (2015-19)

Drama, school life, slice of life, shounen
Has aro/ace characters

Licensed as as Bloom into You by Seven Seas Entertainment.

Kanata no Astra
彼方のアストラ (2016-17)

Comedy, drama, sci-fi, shounen
Has an intersex character

Licensed as Astra Lost in Space by VIZ Media.

Bokutachi LGBT
ぼくたちLGBT (2016-18)

Slice of life, seinen
Has bi, gay, trans characters
Written by a bisexual author
Biographical

Currently not licensed.

Otokonoko Doushi Renaichuu.
男の娘どうし恋愛中。(2017)

Comedy, drama, ecchi, slice of life, mature
Has a pansexual protagonist
Autobiography

Currently not licensed.

Ano Yoru no Pool
あの夜のプール (2018)

Slice of life, seinen
Has an aro/ace character

Currently not licensed.

Madoka no Himitsu
まどかのひみつ (2018-19)

Comedy, slice of life, josei
Has an intersex character

Licensed as Madoka's Secret by Fantasista Inc.

Seibetsu "Mona Lisa" no Kimi e.
性別「モナリザ」の君へ。(2018-22)

Drama, school life, slice of life
Has an aro/ace character

Licensed as The Gender of Mona Lisa by Square Enix.

Mine-kun wa Non-Sexual
峰くんはノンセクシャル (2019)

Drama, slice of life
Asexual protagonist

Licensed as Mine-kun is Asexual by Irodori Comics.

30-sai de "Seibetsu ga, Nai!" to Hanmei shita Ore ga Around Fifty ni Natte Wakatta Koto.
30歳で「性別が、ない！」と判明した俺がアラフィフになってわかったこと。(2019)

Slice of life, comedy
Autobiography
Written by a trans intersex author

Licensed as At 30, I Realized I Had No Gender by TokyoPop.

Senpai wa Otokonoko
先輩はおとこのこ (2019-21)

Comedy, school life, slice of life, seinen
Has bi characters

Licensed as Senpai Is an Otokonoko by Webtoon Entertainment.

Kieta Hatsukoi
消えた初恋 (2019-22)

Comedy, school life, shoujo
Bi protagonist

Licensed as My Love Mix-Up! by VIZ Media.

Watashi wa Kabe ni Naritai
わたしは壁になりたい (2019-23)

Drama, slice of life, josei
Aro/ace protagonist, has a gay character

Licensed as I Want to Be a Wall by Yen Press.

Tomodachi Kekkon
ともだち結婚 (2020)

Drama, slice of life
One protagonist can be interpreted as bi and/or ace

Currently not licensed.

Kimi no Sekai ni Koi wa Nai
きみのせかいに恋はない (2020-21)

Drama, school life, slice of life, josei
Has an asexual character

Licensed as Is Love the Answer? by Kodansha.

Seikyouiku 120%
性教育120％ (2020-21)

Comedy, school life, slice of life, seinen
Has bisexual, lesbian, asexual characters

Licensed as Sex Ed 120% by Yen Press.

Last Gender: Nanimono demo Nai Watashitachi
ラストジェンダー ～何者でもない私たち～ (2021-22)

Drama, slice of life, seinen, 18+
Features many different identities across the LGBTQ+
Discusses heavy topics

Licensed as Last Gender: When We Are Nameless by Kodansha.

Hadashi no Seimei
裸足のせいめい (2022)

Drama, school life, josei
Aromantic protagonist

Currently not licensed.

Ame ga Shinai Koto
雨がしないこと (2023-...)

Drama, slice of life, seinen
Aromantic protagonist

Currently not licensed.