It happened around 4:50 am just south of Avenue 96.
The California Highway Patrol says a driver in a 2011 Mitsubishi Outlander tried to avoid hitting the man has he crossed, but the two collided.
The man died at the scene, authorities say. Officers were investigating to determine why he was trying to cross the highway.
The driver stayed at the scene and cooperated with officers. CHP officials say drugs or alcohol were not factors in the collision.
Part of northbound Highway 99 was closed for about two hours but has since reopened.