Police say the accident took place Friday afternoon at the Pines Bible Camp in Grand Forks, B.C., 523 kilometres east of Vancouver and near the border with the United States.
They say that during the storm, winds snapped off trees, causing two to fall through the roof of a hut, crushing the boy who was inside.
Police say several other children were also injured during the incident.
About 65 children were attending the camp at the time, and the RCMP say victim services has called in counsellors to help the boy's family and other youths.
Police have not yet released the name of the boy who they say is a resident of the nearby community of Christina Lake, B.C.