Most of the victims died instantly when lightning hit the church in the southern district of Nyaruguru, local mayor Habitegeko Francois told AFP.
Two people died from their injuries, and 140 people were rushed to hospital and health centres.
Lightning also killed a student in the area on Friday, the mayor said.
The weather accident in the mountainous region near the border with Burundi took place around midday on Saturday while parishioners of the town of Gihemvu were at a church service.
