Looking for a manga with an androgynous looking character who doesn't really care about their gender, like sometimes they get mistaken for a male when they're actually a female or vice versa.
Kinda like Haruhi from Ouran Koukou Host Bu

Id

Akuma no Riddle if you want a slightly trashy lesbian assassin manga.

Rurouni Kenshin if you want a classic samurai manga.

Shounen Oujo if you want a fantasy with royal intrigue.

Prunus Girl if you want a romantic comedy.

FaLLen if you want a magical girl story.

There's also an androgynous side character in Gekkan Shoujo Nozaki-kun. Since it's an ensemble series, she shows up pretty frequently.

he is not really like that anymore but the MC in Hakkenden - Touhou Hakken Ibun used to have to dress up as a girl when he was younger and does not really care if he gets mistaken for a girl.

and i have not read it but Hanamatsuri looks like it might fit as well.

[img]http://24.media.tumblr.com/3b280fafb72cad0f718be64368e64ca7/tumblr_myylzmuiY41rw3pzao4_250.gif[/img]
Like educational manga? take a look at Ed U. Manga's list of manga here

All these feature major male characters (though not always the protagonist himself) who look like/are mistaken for/dress up as girls:

Boku Wa Ne
Butterfly
Gin no Yuusha
A Night of a Thousand Dreams
Hi Izuru Tokoro no Tenshi
Houseki no Kuni
Pure Blood
RG Veda
Yama Fu-Tang
Bokura no Hentai
Princess Princess -- All the male MC's crossdress; some hate it, some don't mind.
Kiss Me Princess
Kunisaki Izumo no Jijou -- He resents it at first, but eventually comes to accept and even make use of his "ability."
Ditto for Coda.
Chevalier
Honey^2 Skip!

As for girls being mistaken for/pretending to be boys:

Aoharu x Kikanjuu
Flower Flower
Hatshepsut
Gold Rush 21
Renai Idenshi XX
Hakodate Youjin Buraichou Himegami
Joan
Paros no Ken
Oniisama e...

Claudine...! and Double House feature crossdressing women, but they're both transmen, and I don't think you had that in mind when you made this request. Yuureitou also features gender identity issues and doesn't just ignore the gender bending or treat it as a typical everyday thing, so if you're not looking for something that takes itself seriously on that front, you might want to skip those. The same applies for the male-to-female cross-dressing manga Bokura no Hentai that I mentioned above.

Thank you for the recommendations! I don't mind trans characters just as long as they're portrayed in a positive image! 😛

I know this is an old post but I have to recommend "tensei shitara slime Datta ken".

It is an isekai.... I know, I know- but! It's actually really good unlike most isekai and it's the reason why I am looking for more androgynous MCs myself. Also they aren't the main character but check out soul eater, a bit later into the story a character called chrona is introduced. The author hasn't confirmed the sex of chrona, so they are considered as neither a girl or a boy by most of the fanbase, which is what the author wanted. Oh and watch HxH (hunterXhunter) as well, as the author enjoys playing around with gender, sex and the like. The MC's best friend's little brother looks like a girl for example however he is acknowledged as a boy by everyone around him.

Seibetsu "Mona Lisa" no Kimi e

Kimi No Neiro
Charming Junkie

"Bravery we all have it"

Genderless Danshi ni Ai sarete imasu.