Heat transfer phenomenon from a solid surface to a fluid medium is severely dependent upon the mixing process inside the boundary layer. Hence, any mechanism which could increase the boundary layer mixing, results in enhancement of heat transfer phenomenon. Previous studies have shown that the pulsatile jets generated by SJAs can increase the heat transfer efficiency. However, to design an efficient SJA-based heat transfer mechanism, some parameters such as jet frequency and jet exit location must be studied. This paper aims at investigation of the effects of SJA frequency on heat transfer in a rectangular duct with hybrid flow. Despite the normal heat removal systems, the SJA exit is located at a distance from the duct inlet, which adds some complexities to the flow stream and can improve or deteriorate the heat transfer efficiently. The model which is studied in this model uses optimum frequency and gap values. The results are presented in the form of streamlines, temperature and turbulence intensity.