It happened at the diner in the 2100 block of Cedar Creek Road just off Interstate 95.
Police said no victim was there when officers arrived.
The Fayetteville Police Department has not released details about the shooter or the victim's condition.
Investigators said this is the same Waffle House that was robbed at gunpoint overnight.
In that incident, police said two people came in with a handgun and demanded money. An employee was also robbed of cash. The suspects fled on foot.
No one was injured.
Detectives are asking anyone with information about these individuals to contact Detective J. Frashure at (910) 303-8967 or Crimestoppers at (910) 483-TIPS (8477). Crimestoppers information can also be submitted electronically.