The bandit entered the eatery in the 5800 block of University Avenue shortly before 8 a.m., pointed a pistol at the employee and ordered her to turn over cash.
As the victim began to comply with his demand, the robber hit her on the side of the head with the gun and told her to hurry, according to San Diego police. She then opened the register, and he reached in, grabbed an undisclosed amount of money and fled.
The worker was not seriously hurt, police said.
The thief was described as a roughly 5-foot-6-inch black man in his 20s, wearing black sweatpants, dark-colored cloth gloves and a red cloth wrapped around his face and head, police said.
Anyone with information about the robbery was asked to call San Diego County Crime Stoppers at 888-580-8477 or contact the agency online at sdcrimestoppers.org. Tipsters may remain anonymous and could be eligible for a reward of up to $1,000.