Putting this list together, oddly enough, was inspired by a sweet, sad, lovely coming-of-age story about Mira Levenson, a twelve-year-old British girl of Indian and Jewish descent who's journaling the last month of her beloved grandmother's life (among many other things).
Mira in the Present Tense (Artichoke Hearts in the UK), by Sita Brahmachari
Although the Rwandan Genocide wasn't the primary focus of the book, it was an integral part of Mira's new, more complex understanding of the world (not to mention her crush, Jidé), her discovery and exploration of it was a huge part of her coming-of-age journey, and the scenes of her doing research made me wonder what fiction was out there. (Hence, as I said above, this list.)
In addition to all of the book's other virtues—seriously, it's so, so good—there's also a really nice thread about how her PARENTS react to and deal with Mira's maturation. On the one hand, they want to protect her from the horrors in the world, but on the other, they realize that she's growing up, and that learning about and understanding these hard things (as much as understanding is possible, anyway) is a part of that process. It's just really nicely handled.
I'm so very much looking forward to the sequel, which is out in September.
Broken Memory: A Novel of Rwanda, by Elizabeth Combres 
This one is heavily based on interviews with Rwandan refugees, and chronicles the life of a young Tutsi girl who witnessed her mother's murder when she was five years old. Now fourteen, living with the Hutu woman who took her in, still wracked by nightmares, she has to decide whether or not to testify in Gacaca court. According to the reviews I've read, the prose is quite spare, but Combres doesn't pull punches about the subject matter.
Over a Thousand Hills I Walk with You, by Hanna Jansen
This fictionalized biography, translated from the original German, got multiple starred reviews as well as a Batchelder Award. It's about eight-year-old Jeanne d'Arc Umubyeyi, who was ultimately her Tutsi family's only survivor. The book doesn't only chronicle the violence, but the regular life leading up to it, and oddly enough, every review I've read has made me think of Meg Rosoff's How I Live Now, because the book is narrated by a child who is experiencing all of the trauma of a horrific event, but without any real understanding of the political situation that lead up to it.
Shattered, by Eric Walters
I Learned a New Word Today... Genocide, by Elizabeth Hankins
The descriptions of these sound somewhat didactic to me (the Hankins title alone is pretty cringeworthy), but they both seem to have had decently positive receptions, so, onto the list they go. The Walters is about a fifteen-year-old boy who develops a friendship with a homeless soldier whose last mission was as a peacekeeper stationed in Rwanda; the Hankins is about a fifth grader who discovers genocide isn't just something that affects far away people—it's something that has touched people he knows. These two and the Combres were originally published in Canada.
Others?
