No one was injured during the blaze, which did about $500 damage to Naperville Congregational Church at 1 Bunting Lane.
Naperville police Cmdr. Dave Hoffman on Tuesday would not reveal the age or gender of the accused youth or say whether he or she is a member of the church. Hoffman would say only "police are investigating an apparent arson involving a juvenile."
The fire was set about 11:15 a.m. Sunday after a church service. A written police report indicated it erupted beneath the pulpit while 50 people were down in the basement.
Hoffman said the flames and damage were confined to the pulpit area. The blaze was extinguished "almost immediately" by either a church staff member or worshipper, he said.
The police report classified the crime as "aggravated arson."