The National Weather Service confirmed that a tornado touched down on West Howard Road, southwest of Stockton at 1 p.m. Wednesday afternoon.
At least one property was damaged and some powerlines were knocked out.
The tornado was listed as an EF1 and was on the ground for one mile. The weakest a tornado can be is an EF0.
Thunderstorms started moving into Northern California in the early afternoon. The funnel cloud was spotted near Lathrop.
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The National Weather Service says that Tehama, Glenn and Butte Counties could see severe thunderstorm activity through the afternoon.
The last time a tornado touched down in San Joaquin County was 2005 in Manteca.