Children Of The Atom has lots of these: Sarah from the Modus Operandi arcs certinly counts. Cass and Veronica from the Pro Posturas arcs as well. Jess is an odd case, as she is both the main character of Pro Posturas and not an Action Girl of any kind, instead a Ambadassador.
The female Assassins named but so far not developed by Terry Pratchett in the Discworld. Alice Band, Johanna Smith-Rhodes, Jocasta Wiggs, Joan Sanderson-Reeves, and others, all capable of bringing a woman's gentle touch to the deadliest profession. A good starting point is The Graduation Class
Hermione from Harry Potter and the Methods of Rationality is one, being one of the three generals of the student armies. She's also founded an organization, S.P.H.E.W, the Society for the Promotion of Heroic Equality for Witches, to help other girls become this.
In Horseshoes and Hand Grenades and most of its sideories, many of the female characters have been upgraded to fighters. This ranges from Yuki Jojima using her Hayabusa Plushie to punch people into oblivion, Tomoko Nozama using her snake skin as a whip and minor characters like Rumi Egawa charging toward people and kicking them in the face.
While her female friends are also considered this, Keena Soga in Keena & The Defendants Of Constan Academy is a notable version of this trope. She doesn't need guns or even magic, all she needs are her firsts and kicks and can take as many punches as possible. Remember, she previously was a damsel, and really wanted to prove herself. It took only two chapters for her ass kicking to show up.
In the semi-genderbent Sword Art Online fanfiction story The Kirita Chronicles, the main character Kirigaya Kazuta (the genderbent version of the canon protagonist Kirito) is indeed an action girl.
While all the girls from the canon Naruto series are capable fighters already, they qualify even more so in Kitsune no Ken: Fist of the Fox, with Tenten in particular playing it straight in that she constantly trains and goes out to fight so as to become stronger.
Ever female Power Ranger in Of Love and Bunnies. The standouts are Trini (who scared an entire squadron of Red Rangers into fleeing after they fought Serpentera without her), Kim (who fired an arrow into a fight between the Red and White Rangers), and the girl from the Chinese restaurant (who takes on a swarm of Mooks).
Twenty-year old Mary Jane Watson loves to keep up with the latest fashion trends, is a Twilight junkie and enjoys being the centre of male attention at parties. She's also won dozens of fights as a costumed superheroine, with a Rogues Gallery as long as her arm.
The World of the Creatures: One of the character is Buffy Summers. With seven years of experience, plus supernatural slayer strength, Buffy isn't afraid to go after a troop of cybermen with nothing but her bare hands. The other female characters get shades of this as the story goes on.
Daughter Of The Sun has female warriors, just like in the source material, but one of the most notable would be Skypaw. She's able to fight a bear on her own (with the help of her special powers, however).