A vehicle mounting structure for a fuel cell system containing a vehicle floor; a vehicle skeletal member positioned under the vehicle floor, having floor frames provided on the sides of the vehicle body along the longitudinal direction of the vehicle and a plurality of cross members provided in the width direction of the vehicle and connected to the floor frames; and a fuel cell unit and an auxiliary unit of the fuel cell disposed to be adjacent in the longitudinal direction of the vehicle. The fuel cell unit and the auxiliary unit is each sandwiched from both sides in the longitudinal direction of the vehicle by two of the cross members. This vehicle mounting structure for a fuel cell system prevents the length of piping and the length of wiring from becoming excessively long and improves collisional stabilization.