The boy, 3ft 6in tall, bought some sweets in a bag from an assistant in the shop in Ashton-under-Lyne, Greater Manchester.
But he then pointed what is believed to be a gun at her, handed the bag back and ordered: 'Fill it.'
He fled when the assistant, Hansa Lad, activated the alarm system. She told police that he looked about eight years old.
A Greater Manchester police spokesman said: 'The assistant was frightened and we are treating the matter seriously.'
Mrs Lad, 33, said that the boy handed her 50p and asked for 25p worth of Smarties.
She gave him his change and then a man came in. The boy waited until he had gone, then gave her the bag and told her to put everything in.
'It didn't look like a toy gun to me. I pressed the alarm and he ran. I went after him but he disappeared like magic and I didn't see where he went,' she said.
'It was very strange. You hear about this kind of thing happening but not from little children. It is frightening.'Reuse content