Police arrested 20-year-old Troy Bailey Junior, a former member of the Navy. He was living with the child's mom, at Lemoore Naval Air Station.
Investigators say the couple took the child to the naval base hospital where she was pronounced dead.
At first authorities believed the girl died from sudden infant death syndrome. But x-rays and a CT-scan later showed she suffered a skull fracture and a broken arm.
"In the morning is when they said they found the baby unresponsive," said Sgt. Pete Thompson with the Kings County Sheriff's Department. "It's our belief, the injury actually happened the night before and the baby died during the night due to swelling of the brain from the fracture in the skull."
Bailey was booked into the Kings County jail on charges of homicide and child abuse causing death. Investigators are looking into the mother's role, but right now she remains on active duty.