The Gilliam County Sheriff's Office said the Church of the Nazarene is considered a total loss.
At 4:36 a.m. Tuesday, 20 firefighters were dispatched to the church, located at 600 Main St.
Nobody was hurt.
The church was already undergoing repairs after a suspicious fire on July 9.
Firefighters aren't sure whether the fires are related, but the Oregon State Police's arson unit and the ATF are working with the sheriff's office in investigating.
It's believed the church was the oldest building in downtown Arlington, and that it was built in the 1890s.