The incident happened at about 0635 BST on Sunday, at Thoms Store, in Balwearie Road, Tranent.
One of the men threatened the lone woman shop assistant with a knife and demanded the contents of the till.
The other man took packets of cigarettes from behind the counter. They made off with a small amount of cash and £150 worth of cigarettes.
The first man was 5ft 8ins to 5ft 10ins, with a round chubby face. He was of stocky build, had a local accent and was wearing a black bomber-style jacket.
The second man was 6ft, of slim build, and was wearing dark clothing.
A police spokesman said: "This was a particularly harrowing ordeal for the shop assistant, who was alone when the two men entered the store wearing balaclavas and brandishing a knife.
"We want anyone who was in the area at the time and may have noticed the two men to contact police immediately."
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