Officials say a Toyota struck the woman as she crossed the northbound lanes of the highway between Sultana Drive and Westside Boulevard at around 12:30 a.m.
The driver of the Toyota stopped after the crash and moved the woman to the highway median while awaiting authorities.
The woman died at the scene. Her name has not been released.
Investigators say before the collision, the woman had been in another car with a man going southbound on Highway 99. Their car stopped at the side of the road, and for an unknown reason, the woman got out and ran across the highway.
CHP officials said the driver of the Toyota was not under the influence of drugs or alcohol at the time of the crash.