Fire departments from North Carolina and Virginia responded to the fire around 7:30 p.m. at the High View Baptist Church in the 100 block of High View Church Road in Roxboro.
Pastor Avery Dalton told ABC11 that the blaze started in a gable above a second floor classroom.
He said a youth group usually meets in that area on Wednesday evenings, however, they were not in there at the time because they were on a retreat.
About 35 people were in the church attending a weekly night service when, Dalton said, the lights flickered and they started smelling smoke. The pastor said it gave everyone enough warning to get out of the church safely.
"Fire purges according to scripture, so I'm in hopes that God is going to do something wonderful through this, not just for our people, but for the church and in the community," Dalton said. "I've already had two or three pastors come and offer us their facilities and ask how they could help. I've been contacted by probably a dozen pastors tonight."
The church sustained heavy damage. Dalton said parts of the building were more than 70 years old, and that they will rebuild.
"God is sovereign," said Dalton. "We don't always understand everything, but I trust him. I know the Lord is going to do something great through this."