A roof panel assembly of a vehicle may include a roof panel made of composite material and assembled in a vehicle roof, and a center rail attached to the bottom surface of the roof panel. Both side end portions of the roof panel is assembled with roof rails of the vehicle. The center rail includes both end portions connected to roof rails of the vehicle, respectively. The roof panel further includes an auxiliary rail attached on the bottom of the roof panel and placed at a location spaced apart from the center rail at a rear side in the fore and aft direction of the vehicle.