I've been reading Terry Pratchett's The Wee Free Men with DS. The main character is a girl, and a typical Pratchett protagonist - intelligent, cool headed, and brave. A fair few of the main series of Discworld books also have strong female characters and protagonists (notably the Witches books), if you think he's old enough for them.
You might want to look at David Weber's Star Kingdom series ( A Beautiful Friendship, Fire Season, and Treecat Wars ), a young adult series set in his Honor Harrington universe about the early days of contact between humans and treecats. I've only read the short version of A Beautiful Friendship that appears in one of the main series anthologies, but I think it'll tick your boxes. The main series would too, except I'd say it's too adult for a twelve year old (read at least as far as the destruction of Blackbird base in Honor of the Queen before disagreeing).
Diane Duane's So You Want To Be a Wizard series is excellent urban fantasy/SF. The main character is a girl who's about fourteen at the start of it, if I remember right, and her younger sister steps into the limelight a few books in. I thoroughly enjoyed the first four as a teenager, but I haven't read the more recent ones.
Madeleine L'Engle's A Wrinkle In Time series is yet more SF (you might spot a theme in my recommendations...) with different main characters as you go along, but at least three of the five have female leads. The first two are about a teenage girl called Meg, and the last about her daughter. And at least some of L'Engle's Austin Family books (non-SF, for once) follow the teenage daughter of the family.