Because of the ability of stem cells to self-renew and differentiate into cardiomyocytes, they are optimal cell sources for cardiac tissue engineering. Since heart cells experience cyclic strain and pulsatile flow in vivo, these mechanical stimuli are essential factors for stem cell differentiation. This study aimed to investigate the effect of a combination of pulsatile flow and cyclic strain on the shear stress created on the embryonic stem cell layer with a elastic property in a perfusion bioreactor by using the fluid-solid interaction (FSI) method. In this study, the frequency and stress phase angle had been assumed as a variable. The results show that the maximum shear stress at frequencies of 0.33, and 1 Hz and with frequency differences in cyclic strain (0.33 Hz) and pulsatile flow (1 Hz) are 0.00562, 0.02, and 0.01 dyn/cm², respectively. Moreover, in the stress phase angles 0, , and , the maximum shear stress are equal to 0.00562, 0.009, and 0.014 dyn/cm², respectively. The results of this study can be an effective step in developing cardiac tissue engineering and a better understanding of the effects of mechanical stimuli on stem cell differentiation.