The Henderson Police Department said officers were called to the United Prayer of Faith Holiness Church, at 127 Miriam Street, at 9:52 p.m. Thursday night.
Investigators said Barry Wilkerson, 28, of 1304 Nicholas Street, Henderson was found dead of an apparent gunshot wound.
The investigation was ongoing.
Police said there were no church-related activities going on at the building at the time.
Anyone with information is asked to call Crime Stoppers at (252) 492-1925.