Eon by Alison Goodman (used, paperbacck)

Twelve-year-old Eon has been training for years. His intensive study of Dragon Magic, based on Oriental astrology, involves two kinds of skills: sword-work and magical aptitude. He and his master hope that he will be chosen as a Dragoneye - an apprentice to one of the 12 energy dragons of good fortune.

But Eon has a dangerous secret. He is actually Eona, a 16-year-old girl who has been masquerading as a 12-year-old boy for the chance to become a Dragoneye.

Females are forbidden to use Dragon Magic; if anyone discovers she has been hiding in plain sight, her death is assured. When Eon's secret threatens to come to light, she and her allies are plunged into grave danger and a deadly struggle for the Imperial throne. Eon must find the strength and inner power to battle those who want to take her magic...and her life.