: This paper analyzes the fundamental cause of performance degradation in extended back-EMF (EEMF)-based sensorless control under synchronous PWM operation and proposes a compensation method to address this issue. In synchronous PWM, the control period varies in real time depending on operating conditions and changes abruptly, particularly during pulse number transition intervals. If these characteristics of the variable control period are not properly reflected in the sensorless control algorithm, a time-reference mismatch arises between the voltage and current signals used in the EEMF observer. As a result, rotor position estimation errors accumulate, leading to degraded synchronization and sensorless control performance as well as the occurrence of current surges. The proposed method systematically compensates for the time delay characteristics of the input variables caused by the variable control period, thereby maintaining the position estimation accuracy of the EEMF observer and ensuring continuity of the current response even during pulse number transitions. In addition, the proposed approach improves synchronization performance and torque production. Experimental results obtained using a 332-kW IPMSM validate that the proposed method effectively preserves synchronization and suppresses current surges during sensorless operation, confirming its suitability for reliable operation in high-power propulsion systems.