This paper proposes a cooling system using thermoelectric elements for improving the output of building integrated photovoltaic (BIPV) modules. The temperature characteristics that improve the output of a BIPV system have rarely been studied up to now but some researchers have proposed a method using a ventilator. The efficiency of a ventilator depends mainly on the weather such as wind, irradiation etc. Because this cooling system is so sensitive to the velocity of the wind, it is unable to operate in the nominal operating cell temperature (NOCT) or the standard test condition (STC) which allow it to generate the maximum output. This paper proposes a cooling system using thermoelectric elements to solve such problems. The temperature control of thermoelectric elements can be controlled independently in an outdoor environment because it is performed by a micro-controller. In addition, it can be operated around the NOCT or the STC through an algorithm for temperature control. Therefore, the output of the system is increased and the efficiency is raised. This paper proves the validity of the proposed method by comparing the data obtained through experiments on the cooling systems of BIPV modules using a ventilator and thermoelectric elements.