Residents from Chula Vista to Oceanside reported a large rumble around 12:45 p.m.
The mysterious sensation was described by some people as sounding like a door slamming while others said it was strong enough to rattle windows.
A check of the U.S. Geological Survey website showed no earthquake activity.
Two months ago, when San Diegans heard a similar sound, there was evidence of chaff on weather radar. Chaff is a material sometimes emitted during military exercises.
On Friday, however, Tina Stall with the National Weather Service said there was no visible chaff in the area at the time the noise was reported.
The mysterious sound had both residents and experts scratching their heads