Robeson County detectives arrested 28-year-old Jahaziel Levi Rodriguez Vazquez Thursday. Officials said Vazquez also used the alias Armando Pacheco.
At the time of the rape, Rodriguez was 27 years old and worked at the church. The victim was 12 years old.
Detectives are not releasing the name of the church because they believe there may be other victims.
Rodriguez is charged with statutory rape. His bond was set at $50,000.
Anyone with information is asked to call the Robeson County Sheriff's Juvenile Division at (910) 671-3140.