The clerk at the 501 N. San Mateo Drive store was confronted by a male wearing a skull mask, a tan military-style jacket and dark pants about 12:45 a.m., according to police.
The suspect threatened the store clerk with a large knife and demanded money. He then took an undisclosed amount of cash and fled on foot south on San Mateo Drive, according to police.
Police searched the area but were unable to locate the suspect.
The suspect is described as a man about 6 feet tall and approximately 180 pounds. He appeared to have brown hair.
Anyone with information is asked to call San Mateo police at (650) 522-7650 or (650) 522-7676, or to text a tip anonymously to (650) 262-3473.
Community members are advised to not approach or confront the suspect themselves, but instead to contact police.