The blaze started just after 2 a.m. at the more than 160-year old Yaphank Presbyterian Church on Main Street in Yaphank, Suffolk County, hours before Sunday's service.
Firefighters say the fire started in the back of the church and quickly engulfed the building to the steeple.
The massive flames and large amount of smoke made it impossible for firefighters to get inside, and power lines outside made it difficult to get ladders up to the church.
"The walls are there, but nothing is there inside," the Rev. Glorya Johnson said later Sunday. Church leaders were still assessing the extent and cost of the damage, she said.