The blaze broke out around 1:30 a.m. at the Apex United Methodist Church in the 100 block of South Hughest Street.
Several fire crews from Apex, Raleigh and Holly Springs responded to the two-alarm fire at the block-long church.
The blaze was quickly put out. There was no major damage, but there was some damage inside an auxiliary building that is used for afterschool care, Sunday school classes and programs for the homeless.
Pastor Gray Southern told ABC11 that the fire was confined to one room upstairs and there was just smoke and water damage elsewhere.
Southern optimistically said the damage should only impact them for a few days.
"The afterschool program is going to go to a different location on our campus and by Sunday we will be up and going again," he said.
There was no damage to main church sanctuary.
It is unclear what sparked the blaze.