Story Theives! There are two main characters, one is a boy and one is a girl. It's actually a series, but I've only read the first one...

Oh! And there's also my favorite books of all time, The Land Of Stories! Again, one main is a boy and one is a girl, but there are also a lot of female supporting characters. I just got the last book in that series yesterday, and so far it is AMAZING...

Anyways, enough about my book rant, and I hope that I could help!

Keeper of the Lost Cities! By far my favorite series, and main character is Sophie Foster, a girl!

In terms of young adult books, anything by Sarah J. Maas. Her writing is amazing and wonderfully unpredictable, and she has some wonderful character, both female and male, but her books are definitely for a more mature age range. Just some things I reccomend. And stuff by Marissa Meyer, which is a little less YA, but still really good. Then there's the ever dark, but not too mature, Leigh Bardugo. Just some reccomendations (logically, it's what you asked for) of books that I find really good. No pressure to read them or anything.

Lunar Chronicals! Those books have a lot of very strong, diverse, female leads. And the series is simply epic, so there's that incentive to read them as well.

Akata Witch by Nnedi Okorafor

Listening for Lions by Gloria Whelan

Heaven Eyes by David Almond 

the Water Mirror/Dark Reflections trilogy by Kia Meyer

Twelfth Night by Shakespeare

The Girl Who Drank the Moon by Kelly Barnhill

Flora and Ulysses by Kate DiCamillo

The Book Thief by Markus Zusak

A Natural History of Dragons (and its four sequels) by Marie Brennan

The Cabinet of Wonders by Marie Rutkoski 

The Girl Who Could Fly by Victoria Forester

The Mark of the Dragonfly by Jaleigh Johnson

Adventures of a Cat-Whiskered Girl by Daniel Pinkwater

The Ordinary Princess by M.M. Kaye

The Princess Academy trilogy by Shannon Hale

Awkward by Svetlana Chmakova 

I recommend the Grisha Trilogy by Leigh Bardugo! It takes place in an expertly constructed fantasy world based on Tsarist Russia. The main character is Alina Starkov, and the story is told from her perspective, framed with third-person chapters.

Also, the Six of Crows Duology, a sequel of sorts to the GT, has six main characters, two of which are brilliant, strong, well-developed female heroes, who love and fight and aren't just pretty lampshades. They're some of my favorite female characters that I have ever encountered.

Sarah J. Maas' Throne of Glass books (Epic Fangirl mentioned her as well) has a female protagonist. I've never read the books myself, but I've heard that they are very good. 

Both The Hunger Games and Divergent are dystopian novels with female protagonists. I didn't love the latter (Veronica Roth's writing just seemed dry to me) but a lot of people do, and Tris is pretty cool.

To Kill a Mockingbird by Harper Lee. We had to read this book in school last year, and it was one of the few "assigned reading" novels that I truly loved. If you haven't read it, I deeply recommended it.

The Matched series by Ally Condie has a female MC— Cassia. She's a is a strong character, a revolutionary willing to defy the laws of her society, but I didn't like the books too much. The dystopian romance genre just isn't my thing, and this one to me was particularly a snore-fest. But if you enjoy this genre, you may enjoy this book, too.

Oh, I thought of some more!

The Song of the Lioness quartet! Actually, anything at all by Tamora Pierce, who is an amazing writer and always has really amazing, independant female characters. This series, and many of her other books as well, does have some mature-ish stuff so I would advise anyone younger than twelve to wait a little while.

The Golden Compass is also wonderful and has an epic girl lead. Lyra is one of my favorite characters ever, and I would recommend this book to anyone.

The Penderwicks by Jeanne Birdsall is centered around 5 girls and 1 boy. It has some sequels too.