Flame in the Mist (Flame in the Mist Series #1) by Renée Ahdieh

From the #1 New York Times bestselling author of The Wrath and the Dawn, comes a sweeping, action-packed YA adventure set against the backdrop of Feudal Japan where Mulan meets Throne of Glass.
 
The daughter of a prominent samurai, Mariko has long known her place—she may be an accomplished alchemist, whose cunning rivals that of her brother Kenshin, but because she is not a boy, her future has always been out of her hands. At just seventeen years old, Mariko is promised to Minamoto Raiden, the son of the emperor's favorite consort—a political marriage that will elevate her family's standing. But en route to the imperial city of Inako, Mariko narrowly escapes a bloody ambush by a dangerous gang of bandits known as the Black Clan, who she learns has been hired to kill her before she reaches the palace.

Dressed as a peasant boy, Mariko sets out to infiltrate the Black Clan and track down those responsible for the target on her back. Once she's within their ranks, though, Mariko finds for the first time she's appreciated for her intellect and abilities. She even finds herself falling in love—a love that will force her to question everything she's ever known about her family, her purpose, and her deepest desires.