This study describes a forced convection heat transfer coefficient on a heat transfer surface in the flow separation area by pulsating flow. The effectiveness of flow pulsation on heat transfer enhancement in the flow separation area has already been reported. An understanding and a performance modeling of the heat transfer coefficient becomes essential to apply the pulsating flow to the thermal equipment. This paper investigated the relationship between the pulsating flow condition and the heat transfer on the heating surface sandwiched between two square cross-section channels and where flow separation was caused through 3D-CFD analysis. In the range of the paper, the research found that the pulsating flow's heat transfer performance on the flow separation area is affected by the time-averaged Reynolds number and the pulsating frequency. The prediction formula can be developed to calculate the time-averaged Nusselt number using the pulsating Strouhal number.