Churchgoers were celebrating a group of children's first Communion, which was being livestreamed at St. Mary Magdalen Church in Abbeville.
Parishioners immediately confronted the armed teen and took him outside. They then called police.
Footage of the livestream shows a priest duck behind an altar as parishioners stand up to see what was going on. Several altar boys run behind the priest amid the panic.
No one was injured in the incident.
The 16-year-old is facing charges of "terrorizing" and possessing a firearm.
"I'm hurt. I'm angered. I'm disappointed, but this is a society problem, not a local problem," Abbeville Councilman Brady Broussard Jr. said.
Abbeville Police Department Police Chief Mike Hardy is praising the parishioners and the clergy for their quick response and remaining calm throughout the ordeal.