Introduction The superiority of pulsatile or non-pulsatile perfusion in cardiopulmonary bypass (CPB) regarding morbidity and mortality is still debated. Therefore, we aimed to investigate the effect of different pulse rates in pulsatile perfusion in patients undergoing coronary artery bypass graft (CABG) and compared it with non-pulsatile perfusion. Materials and Methods In this randomized clinical trial, 90 patients who were all candidates for CABG under CPB were enrolled. Patients in groups A and B received pulsatile perfusion with 30 and 70 pulses per minute, and group C received non-pulsatile perfusion. The biochemical and clinical parameters in the ICU were evaluated in the study groups. Results There was no statistically significant difference between patients' clinical outcomes and kidney and liver function markers (all Ps> 0.05). Mean serum lactate level increased but did not show a statistically significant difference between the study groups ( p = 0.8). The mean urine volume at 12 and 24 h after surgery was higher in group A, but there was no statistically significant difference between the three groups during the study period ( p = 0.3). No significant difference was found in the length of the ICU stay between the study groups ( p = 0.2). Conclusion Our studied parameters demonstrated no significant difference between pulsatile and non-pulsatile and between 30 and 70 pulse rate pulsatile perfusion methods. Our findings support that pulsatile perfusion with different pulse rates has no advantages over non-pulsatile perfusion in selected CABG cases.