The county coroner's office identified her as nine-year-old Karen Perez of Concord.
The girl also had another bacterial infection. State and county health officials are studying what role it may have played in her death.
A San Bernardino County man and a Los Angeles County woman also diagnosed with the virus died in May.
According to the Centers for Disease Control and Prevention, 20 swine flu-related deaths have been reported nationwide.
State officials say California has seen about 576 cases of the virus.