A man believed to be aged in his 20s entered Costcutter on Heworth Road at around 12.45pm yesterday (Wednesday) and passed the cashier a note demanding money from the till.
He then showed the cashier the gun he had in the waistband of his trousers.
The contents of the till were subsequently handed over and he left the store.
The robber is described by police as skinny, around 5ft 10ins, with short blonde or ginger hair. He was wore a khaki-coloured hoody with a zip front.
Officers from North Yorkshire Police are reviewing CCTV footage from the area and conducting door-to-door enquiries as part of their investigation.
Detective Inspector Jackie Smart said: “Our detectives are working around the clock on this investigation but members of the public may have vital information that could help us.
“This incident happened in a relatively busy residential area at a time when people will have been out and about. So if you saw anything suspicious, no matter how insignificant it may seem, we’d like to hear from you.”
Detectives believe members of the public may have seen two men shouting nearby before running down Dales Lane. One continued down Dales Lane while the other turned right and ran into Harrison Street. They want to speak to anyone who witnessed this.
One of the men is described as 5ft 11ins, of medium build with short dark hair, tight blue jeans and a greyish hoodie. He wore blue and white trainers.
The second man was shorter, about 5ft 7ins, of medium build and with short light brown hair. He wore dark blue jogging bottoms, a green cardigan with a zip and a light-coloured t-shirt underneath.
Investigators have yet to establish whether they were involved in the incident.
Anyone with information that could help the investigation is asked to call the York Serious Crime Team on 01609 643279 quoting reference number 12180130457 when passing on information.