The burglary was reported at 9:40 a.m. at the South Bay Baptist Church at 960 Fifth Ave., Lt. Phil Collum said.
"This morning we entered the building and found our lighting, the lighting board and 24-channel audio board were missing," said Scott Johnston, the church's worship and choir director.
A $2,000 drum set, more percussion equipment worth nearly $1,000, two 15-inch speakers and two slant monitors, used by musicians so they can hear their performance, were also taken, Johnston said.
He said it appeared the burglars jumped a nine-foot fence at the church school, where some smaller items were taken.
The items had to be passed over the fence, so there must have been several burglars involved who knew what they wanted, according to Johnston.
"We prayed for them (during services)," Johnston said. "We feel sorry for them. We're in the business of forgiveness."
The church has insurance for the missing items and officials are looking into installing alarm systems that connect to the Chula Vista Police Department, he said.
Meantime, he said he is working on backup systems in time for a graduation ceremony scheduled Thursday for the church's school.
Collum said officers searched the church property for fingerprints. The lieutenant said there was no sign of forced entry and no information about suspects.