The incident took place at 2.15pm on Saturday (September 29). The suspect stole cash from the till and left the shop on foot.
"The man was wearing a heavy brown coat with a hood and baseball cap. We couldn't see his face. He was around five and a half feet tall and emptied the till - a couple of hundred euro was taken," a shaken member of Jaybees staff told Waterford Live.
Anyone with information should contact Waterford Garda Station on 051-305300.