The boys, aged 12, 13 and 14 were charged with one count of second-degree arson. Police said the boys were burning materials near the church when the building caught fire.
Fire investigators said the roof of the 81-year-old church sustained most of the damage. Parishioners said the church had a decorative tin ceiling that dated back to 1923.
Fire crews were dispatched to the scene in rural Reisterstown at about 12:45 a.m. The first engine called for backup after finding heavy burning through the roof.
Firefighters battled the blaze inside the building and brought it under control within an hour. One firefighter sustained a minor injury and was treated at the scene.
No one was in the church at the time of the fire.
More than six Baltimore County units responded as well as several units from Carroll County.