No one was inside the church when the fire broke out, nor was anyone hurt during the incident.
Highway 95, the main road through Fountain City, was closed for more than two hours as crews fought the fire.
The church is part of the Diocese of La Crosse. Director of Communications and Public Relations Jack Felsheim said that until further notice, Mass will be celebrated at the Parish Life Center near the church following the regular schedule.
While there was some fire damage, smoke damage spread throughout the entire church.
The statement from the Diocese said the structural integrity of the church wasn't damaged.
Clean up efforts will start once the investigation into the fire's origin is complete.
The Buffalo County Sheriff's Department is leading the investigation into the fire. The department asked anyone who might have seen or noticed anything before the fire to contact them at 608-685-4433.