Garner was sworn in as chief in August of 2020.
His last day with the department was Monday.
City Manager Nathan Olson did not comment or specify a reason for Garner's departure.
Olson says the search for a new chief will begin immediately.
Commander Joshua Johnson will serve as acting police chief.
Garner was also the police chief of Selma for six years and is also a 34-year veteran of the Fresno Police Department.