Merseyside Police said they threatened staff at the shop in Huyton with knives before escaping with cash and cigarettes on Sunday afternoon.
The raid took place at 15:45 BST at Gentwood Mini Market on Gentwood Parade.
The younger boy wore grey jogging trousers and a green jacket while the older had dark clothing.
Two boys, one believed to be as young as 12 and the other thought to be 15, robbed a shop at knifepoint.