The optimal right ventricular (RV) pacing site during pacemaker implantation is still unclear due to left ventricular (LV) dyssynchrony by traditional RV pacing. His-bundle (HIS) pacing has achieved narrow QRS and maintained LV synchrony but high failure rate. RV septal pacing occasionally has QRS waveform with wide and narrow component in the early and late phase, respectively, and maintains LV synchrony, reflecting the normal conduction system. We aimed to define this QRS waveform as retrograde penetration pacing into the conduction system (RPP-CS) and compared its effect on LV synchrony as an alternative approach of HIS pacing.We enrolled 42 patients with atrio ventricular block (AVB) or bradycardia atrial fibrillation (AF) requiring pacemaker implantation (RPP-CS, n = 27; no RPP-CS, n = 15). Baseline characteristics were similar between the groups. RPP-CS was observed in 96% and 26% of the RV septum and apex area, respectively. RPP-CS had a significantly shorter QRS width (p < 0.001). The frequency of maintaining LV synchrony was significantly higher in RPP-CS (67% vs. 20%, p = 0.003). The QRS interval's optimal cut-off value during RPP-CS was 132 ms for prediction of LV synchrony (sensitivity 83%, specificity 89%, positive predictive value 94%, and negative predictive value 73%). During RPP-CS, shorter QRS intervals (QRS ≤ 132 ms) had better postoperative LV ejection fraction than longer intervals (p < 0.001).RPP-CS, especially with short QRS intervals (≤132 ms), had a high frequency of LV synchrony, maintained postoperative cardiac function, and may be an adequate first-line RV pacing site strategy for AVB or bradycardia AF as an alternative approach of HIS pacing.