Non-binary Manga part 1
Manga
Some manga that features a non-binary/x-gender character. Some are headcanons- those are indicated by question marks.
Part 2: https://myanimelist.net/stacks/37987
Extra non-binary manga that's not on MAL (yet):
Onna no Karada ga Iya nano de Mune wo Torimashita
Kazuki (x-gender) (protagonist)
Then I saw RuPaul's Drag Race': coming out as X-gender in Tokyo
M. A. Joy (x-gender) (protagonist)
Kyouhaku sei Shougai desu!
Asuka Miyazaki (x-gender) (protagonist)
Kyouhaku sei Shougai Chiryou Nikki
Asuka Miyazaki (x-gender) (protagonist)
Unknown Color
Chiaki Hinaga (non-binary) (protagonist)
Quintet×Question
Mokuba Ao (x-gender) (main)
Bloody Chinatown
Kanaya (gender-free) (main)
Bara Shishaku
Gideon (genderless/gender ambiguous?) (main)
Part 2: https://myanimelist.net/stacks/37987
Extra non-binary manga that's not on MAL (yet):
Onna no Karada ga Iya nano de Mune wo Torimashita
Kazuki (x-gender) (protagonist)
Then I saw RuPaul's Drag Race': coming out as X-gender in Tokyo
M. A. Joy (x-gender) (protagonist)
Kyouhaku sei Shougai desu!
Asuka Miyazaki (x-gender) (protagonist)
Kyouhaku sei Shougai Chiryou Nikki
Asuka Miyazaki (x-gender) (protagonist)
Unknown Color
Chiaki Hinaga (non-binary) (protagonist)
Quintet×Question
Mokuba Ao (x-gender) (main)
Bloody Chinatown
Kanaya (gender-free) (main)
Bara Shishaku
Gideon (genderless/gender ambiguous?) (main)

Manga, 5 vol, 2018
Me:-
Author:9
Mogumo (agender) (protagonist)
Yamashiro (non-binary?) (minor)
Yamashiro (non-binary?) (minor)

Manga, 2 vol, 2020
Me:-
Author:7
Asuka Miyazaki (x-gender) (protagonist)
The General of Old (x-gender) (supporting)
Beautician (x-gender) (minor)
The General of Old (x-gender) (supporting)
Beautician (x-gender) (minor)

One-shot, ? vol, 2018
Me:-
Author:8
Makoto Saotome (bigender) (protagonist)
Yuuko Kanzaki (agender) (main)
Yuuko Kanzaki (agender) (main)

Manga, 2 vol, 2020
Me:-
Author:7
Poppy Pesuyama (x-gender) (protagonist)
Kemomi (x-gender) (supporting)
Kemomi (x-gender) (supporting)

Manga, 2 vol, 2017
Me:-
Author:-
Poppy Pesuyama (x-gender) (protagonist)

Manga, 10 vol, 2018
Me:-
Author:6
Hinase Arima (agender, sexless) (protagonist)

Light Novel, ? vol, 2000
Me:-
Author:-
Kino (agender) (protagonist)

Manga, ? vol, 2021
Me:-
Author:5
Mihaya Hayami (genderfluid?) (main)

Manga, 1 vol, 2016
Me:-
Author:7
Tamaki Ookawa (non-binary or trans man) (main)

Manga, 15 vol, 2002
Me:-
Author:-
Yoshino Takatsuki (non-binary or trans boy or cis girl) (main)

Light Novel, 1 vol, 2007
Me:-
Author:-
(Name removed for spoilers) (agender and intersex) (main)

Manga, 3 vol, 2021
Me:-
Author:7
Yo (gender questioning/maybe non-binary) (main)
Masanori "Marie Claudia Campbell" Fuwa (bigender) (supporting)
Kakeru (agender) (supporting)
Kei (graygender) (supporting)
Masanori "Marie Claudia Campbell" Fuwa (bigender) (supporting)
Kakeru (agender) (supporting)
Kei (graygender) (supporting)

Manga, 10 vol, 2004
Me:-
Author:-
Mashiro Ichijou (genderfluid? and intersex) (protagonist)

Manga, 7 vol, 2010
Me:-
Author:-
Ayato Godwin (sexless) (protagonist)
Angela (sexless to female) (minor)
Angela (sexless to female) (minor)

Manga, 4 vol, 2015
Me:-
Author:8
Dareka/Someone/Anonymous (agender) (supporting)
Misora (gender questioning/maybe non-binary) (supporting)
Misora (gender questioning/maybe non-binary) (supporting)

Manga, 37 vol, 2016
Me:-
Author:-
Najimi Osana (genderqueer) (supporting)

Manga, ? vol, 2016
Me:-
Author:-
Kanata Okitsu (non-binary) (supporting)

Manga, ? vol, 1998
Me:-
Author:-
Neferpitou "Pitou" (gender ambiguous/maybe non-binary) (supporting)
Kalluto Zoldyck (non-binary?) (supporting)
Nanika/Something (gender ambiguous/maybe non-binary) (supporting)
Kalluto Zoldyck (non-binary?) (supporting)
Nanika/Something (gender ambiguous/maybe non-binary) (supporting)

Manga, ? vol, 2017
Me:-
Author:-
Opera (gender ambiguous/maybe non-binary) (supporting)

Manga, 30 vol, 2018
Me:-
Author:-
Uraume (gender ambiguous/maybe non-binary) (supporting)

Manga, 12 vol, 1996
Me:-
Author:-
Ruby Moon/Nakuru Akizuki (genderless) (supporting)

Manga, 77 vol, 2003
Me:-
Author:-
Kyuubei Yagyuu (genderqueer) (supporting)
Haji (gender ambiguous/maybe non-binary) (supporting)
Daishikyou/Archbishop (agender and intersex) (supporting)
Haji (gender ambiguous/maybe non-binary) (supporting)
Daishikyou/Archbishop (agender and intersex) (supporting)