The fire, dubbed the "Lilac Fire", started around 11:15 a.m. and thick smoke was seen for miles.
All of West Lilac Road now has mandatory evacuation in place.
Authorities say the new fire has destroyed two buildings and damaged 12.
Just as Southern California is enduring strong winds and threats of wildfire this week as a strong Santa Ana system passes through the region, a fast-moving brush broke out in San Diego County.More news: John Lewis to Boycott Civil Rights Museum Opening Due to Trump's Attendance
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San Diego County has proclaimed a state of local emergency in the Fallbrook area. The nearby Sullivan Middle School and Bonsall High School have been evacuated, along with other nearby areas.
Temporary shelters have been set up at Fallbrook High School, the East Valley Community Center in Escondido, Pechanga Casino and Pala Casino, according to CAL Fire.
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Cal Fire units are at scene of the Lilac Fire located at Old Hwy 395 cross of Dulin Rd in Bonsall.