This work proposes a PWM modulation scheme pertaining to sector transitions for three-phase isolated buck-matrix rectifier. PWM modulation schemes realizing UPF (Unity Power Factor) operation and ZVS (Zero-Volt Switching) turn-on at matrix bridge by dividing input AC voltage into sectors are available in existing literature, but issues related to sector transitions are not discussed. The proposed modulation scheme ensures that excessive current or voltage stresses are not experienced by matrix bridge switches during sector transitions. Moreover, synchronous rectification for switches with forward-biased diodes can be performed at matrix bridge using the proposed modulation scheme, not compromising on power conversion efficiency. Analysis of stress causing mechanism at sector transition boundaries is presented along with simulation results. The proposed modulation scheme is verified experimentally and peak efficiency of 97.7% is obtained on an 8 kW, 400 V AC input/50 V DC output converter prototype, while eliminating current stress due to AC source short-circuit and reducing peak drain-source voltage at matrix bridge by 10% during sector transitions.