Officers were responded to reports of being fired shortly after 9 am on Grove Avenue near Cedar and Church Avenues in southeast Fresno.
When police arrived, they found the teen inside a car who had been shot in his left shoulder.
The 16-year-old was taken to Community Regional Medical Center and is expected to recover.
Investigators believe the suspect involved in the attack is a man in his 20s.
A motive for the shooting has not been determined. Officers have blocked off the area while they continue their investigation.
Anyone with information is asked to call the Fresno Police Department.