Just after 8 p.m. ET, a student witnessed the lightning strike and called university police.
The officers saw smoke billowing from the chapel and dialed 911.
Firefighters responded to the scene and brought the blaze under control after about 2.5 hours.
Officials say the chapel was empty at the time and no one was injured.
The small fire was contained to the school’s bell tower.
“We thank the observant and quick thinking student, the responsive officers here at the Mount and the firehouses that sent crews from Emmitsburg, Northern Maryland and Southern Pennsylvania,” said University President Thomas Powell.
“The fireman risked their lives to save our beloved IC Chapel. We give our thanks to God that the fire was contained but mostly we thank God no one was injured and our Mount students are safe.”