Most of the girls of AMARANTO have at least some fighting skill, and participate in various battles throughout the course of the game.
The setup for Aoishiro is the girls' kendo club going on a holiday, so all the "normal" girls are trained in at least ritual combat with wooden weapons. The cast only gets more badass from there. Pretty much everyone except Yasumi and Nami is a fighter, basically.
Tomoyo Sakagami from CLANNAD, making her kinda stand-out in a mostly non-Action anime.
The strongest character in Danganronpa is Sakura Oogami, who has wrestling and martial arts as her special talent.
Kawasumi Mai from Kanon is pretty cool with a sword.
Maji Koi is a World of Action Girls in short skirts with weapons. Apparently the whole city is descended from samurai and they all inherited the warrior spirit?
Being heavily action oriented, the Nasuverse is filled with this, with the main heroines always being one.
Just about all the girls in Kara no Kyoukai, even though it's Shiki who takes the cake.
All girls in Tsukihime except Hisui and maybe Kohaku (unless we count Melty Blood, where they're upgraded to Ninja Maids).
All female Servants (Caster, Saber, Rider) in Fate/stay night, plus Rin Tousaka and Sakura Matou (though Sakura is more of a Dark Magical Girl). Though Type-Venus never had any action scenes and seem to be very gentle, it is extremely likely she can kick a lot of ass as well; even weakened, she is still one of the "Ultimate Ones."
Since the framing story involves a giant battle where the champions of various sub-kingdoms battle for the right to marry the prince, all the girls of Princess Waltz are ridiculous badasses. Even the cute quiet young-looking one. Especially the cute quiet young-looking one.