Mechanically-attached waterproofing system has become popular in Japan. Being vulnerable to wind actions, especially to suctions, this roofing system is often damaged by strong winds. Similarly, photovoltaic (PV) systems installed on flat roofs are often damaged by strong winds, because the PV panels are subjected to large wind forces in an adverse wind. In order to reduce such damage to both systems, the authors propose to install the PV panels parallel to the flat roof with gaps between them, which may reduce the net wind forces on the PV panels due to the effect of pressure equalization. In addition, the wind pressures acting on the waterproofing system will decrease significantly. The present paper investigates the validity of the above-mentioned idea. The wind pressures underneath the PV panels, called ‘layer pressures’, are evaluated by a numerical simulation using the unsteady Bernoulli equation together with the time history of external pressures measured at many locations on the rooftop of a flat-roofed building model in a turbulent boundary layer. The results clearly indicate a significant reduction of wind forces acting on the PV panels as well as on the waterproofing system. The use of PV panels for reducing the wind pressures on waterproofing system is quite effective to the corner region of the roof, where very large suctions are induced in a diagonal wind.