I'm looking for manga where there is a female genius (preferably a main character). She must not just be a plot device, but rather an actual character. For some reason I am having trouble finding captivating female geniuses (or just really smart females). Please help.

And no mecha or ecchi manga.

Akagami no Shirayukihime
Tonari no Kaibutsu-kun
Mahouka Koukou no Rettousei
Okoborehime to Entaku no Kishi

Here are a few:

Ongoing

Cheese in the Trap
Chang Ge Xing
Seigi no Mikata (Not the main character, and she's kinda a plot device since the plot revolves around her)

Complete

Basara (Not a typical genius per se)
Ashita no Ousama
Nodame Cantabile (Piano genius, everything else not so much...)

All of the reccs are either Shoujo or Josei, sad to realize that I don't have any Seinen or Shounen recs with a genius/smart female main character (excluding Chang Ge Xing since it's Seinen in Japan and Shoujo in China).

Must Read Webcomic:
Unsounded

Lists:
Reading
Complete
Western Webcomics

warau kanoko sama ( love it so much)
koi dano ai dano (love it even more)
tonari no kaibutsu kun
Beauty Pop
Maid sama
Thats all I have at the top of my mind 🙂

Shion no Ou
Medaka Box

Then there's always the more action-y ones.

Sengoku Strays
Claymore

Suugaku Girl I haven't read it, but reading the summary, I think it's bound to have smart leads.

Also Karakai Jouzu no Takagi-san has a quite smart female lead, to the point that the entire manga revolves around her successfully pulling pranks and mind tricks on the male lead.

My current top 3:
Fullmetal Alchemist
Pandora Hearts
3-gatsu no Lion

smart female leads:

Kimi wa Pet
Gokusen - already on your reading list

Reinouryoukusha Odagiri Kyouko no Uso fits perfectly. Sadly, it's been dropped (the recent Death Toll release was just a one-off, apparently).
Asamiya-san no Imouto
Alyosha!
Kisshou Tennyo
Nijuu Mensou no Musume (Might want to watch the anime; the manga isn't scanlated)
Online - The Comic
Reizouko Tantei

-- Not all of these girls/women are geniuses, per se, but all of them are protagonists and quite clever/much cleverer than the male lead.

I list as many Female Programmer as i could within 5 minutes in the link so look there and the Ergo Proxy anime counts too. She can also hack...
Try out the tag Smart Female Lead with genres you like and see what happens.
PS: Liar Game ends up revealing that towards the end so how did you overlook it calstine?

Edit: Nao is firstly the protagonist of LG and the manga flat out states that she has the same mental capacities the 2 big brains have at the end. She further outsmarts nearly all adversaries too and i would be surprised if anyone who posted in this topic had her IQ.

I also read EU/US comics and am a librarian.
Manga-Masters, My ANN-Lists + Imdb

Quote from residentgrigo

PS: Liar Gameends up revealing that towards the end so how did you overlook it calstine?

I don't get what you meant by that, actually. In Liar Game Akiyama is the genius, right? And while Nao is an even more important character than him (one of the OP's requirements) and not as stupid as one would initially believe, I don't think she fits this request. And if you mean Fukunaga, well... I'm pretty sure the OP didn't want MtF's, and anyway, Fukunaga rarely dresses or behaves like a woman.

More recs:
Kakegurui
Utsuro no Hako to Zero no Maria (Novel)
Tenkuu Shinpan
Ciel - The Last Autumn Story
xxxHoLic
Trick Ster -- Played for comedy. But she really is very smart, and manipulative, to boot.
Shingeki no Kyojin
Yuureitou
Christie High Tension -- Though if you're familiar with the original Sherlock Holmes stories you should give this a pass.

Steins; Gate (anime)

Basara The female lead is a genius war leader, she often comes up with unexpected strategy to gain upper hand against her opponent.

Steins;Gate The female genius here is partner of a mad scientist who has experimental project about time leap/travel.

Actually the term of 'female genius' is very broad. I don't know what kind of genius that you exactly want since genius characters usually have unique personality along with their brilliancy. In Basara, Sarasa didn't become a leader of her own choice but she turned to be one of the best. She struggled so much during the story, and since she has kind heart she often suffer her wars and cry a lot. But she continue to fight for the dream of her people to the very end. In Steins:Gate, Kurisu is a well versed researcher, being calm and genius herself, she found irresistible presence in Okabe, a self-proclaimed mad scientist, and his research.