David Seth Couick, 16, turned himself in to the Union County Sheriff's Office on Thursday.
Deputies said they began investigating Couick after a tip to DSS earlier this summer.
Couick's father is an associate pastor at Bible Baptist Tabernacle Church in Monroe and helps with the day care at the church's school, Tabernacle Christian.
Couick was a student there last year, and detective said some of the alleged sexual assaults occurred on the church/school campus.
"Some of the things we found are very concerning," said Detective Andy Mullis.
Mullis said the investigation uncovered three victims of sexual assault, boys and girls between 6 and 7 years old.
Couick's father encouraged him to talk to authorities about the incidents, and detectives said he did confess to the crimes.
"I think he was feeling remorseful for what had happened, and I think it had come to the point that he realized what he had done was wrong," Mullis said.
Couick is facing 24 felony counts of indecent liberties with a child and sexual acts with a child.
Church officials released a statement about the assaults on Thursday, saying none of the assaults occurred during school hours or at supervised school functions.
The statement, also sent to parents, read, in part, "In over forty years of serving the community as a church and school, nothing of this magnitude has happened before, and we regret that such an incident has happened now. As a school we have increased protective measures for all students to insure no incident of this or any kind happens while children are in our care."
Couick was released from jail on a $20,000 bond and is under the supervision of his parents.