The man escaped with a small amount of cash from the station in Boglemart Street, Stevenston, North Ayrshire, at around 7.45am on Saturday.
He threatened a 63-year-old worker and demanded money from her before runing off towards Aisla Drive in the town.
The worker was not injured but was left in a state of shock, police said.
The thief wore a navy Nike cap, a black Berghaus jacket, dark trousers and white trainers.
He was also carrying a yellow JD Sports bag.
Detective Inspector Mick Carr said: “Our inquiries are under way to trace the man responsible for this robbery.
“The shop attendant was not injured, but was left in a state of shock following the incident.
“We’ve conducted door-to-door inquiries and continue to assess CCTV to determine his direction of travel following the robbery.
“I would ask anyone with any information to get in contact. You may have seen a man in dark clothing running towards through the houses behind the petrol station.
“You may not think the information you have is much, but as part of our broader investigation, it could really make all the difference.”