The Mariouhna Church Diocese was torched in Asyut, located south of the Egyptian capital of Cairo on Wednesday night.
Twitter users posted images of the church.
Zaid Benjamin, the anchor with Radio Sawa, posted a photo on his account, confirming it is the church.
The photo shows flames creeping up the side of the church.
The fire comes after the most deadly day in Egypt since the fall of former leader Hosni Mubarak more than two years ago. Hundreds of people were killed and the government instilled a curfew.
Islamists clashed with police and troops all day on Wednesday, but it is unclear who torched the church.
A health ministry official told Reuters that 300 people were killed and thousands more were injured.
President Barack Obama and Secretary of State John Kerry released statements condemning the violence.