It happened at the Kangaroo convenience store and gas station on U.S. Highway 15-501 south of Murray Hill Rd. just before 4 a.m.
Investigators said a man covered up in a dark "hoodie" style sweatshirt came into the store armed with a semi-automatic pistol and shot the clerk.
He took money from the register and ran off on foot.
The clerk was taken to the hospital. The clerk's name and condition was not given.
Anyone with information was asked to contact the Southern Pines Police Department at (910) 693-4110.