This study demonstrates fast pulse train switching using a coherent polarization beam combiner with a phase difference detection (PDD) algorithm. Based on the highly stable feedback control obtained with the PDD algorithm, stable burst-mode extraction with an arbitrary duty cycle was achieved with a contrast ratio of 800:1 for a third-harmonic light (347 nm) of a 5 MHz pulsed Yb-doped fiber laser. The proposed method can be effectively used for high-speed switching in high-average-power pulsed laser systems.