Police said the robbery happened around 3:19 a.m. at 2411 Landmark Drive off Lake Boone Trail.
At least two of the suspects entered the store, demanded money from the clerk and took off with cash, police said.
In the 911 call, the CVS worker said all of the suspects were armed.
"The reason I'm calling is because we were just robbed," the caller said. "Three men came in the store, ski masks all kinds of different things on. Uh, they had guns, all of them had guns."
Two employees were in the store at the time and nobody was injured.
A CVS store in Chapel Hill was also robbed on Monday. Chapel Hill police said they are working to determine whether the cases are connected.
Anyone with information is asked to call Raleigh CrimeStoppers at (919) 834-HELP or visit raleighcrimestoppers.org for text and email reporting options. CrimeStoppers pays cash rewards for anonymous tips that help solve cases.