It happened at 2:30 a.m. Thursday morning at Demaree Street and Riggin Avenue.
Police say the deputy was traveling north on Demaree.
That's when a Nissan heading west on Riggin collided with the deputy, striking his passenger side.
The Nissan came to rest in the intersection, while the deputy's vehicle ended up in a grassy area of a nearby church.
The deputy and woman in the Nissan were taken to the hospital with moderate injuries.