The repetitive scanning of a focused laser beam was applied to increase the throughput of particle separation using laser radiation pressure. The relationship between the scanning conditions, specifically laser output power, scanning distance, scanning frequency and the characteristics of particle transportation, was investigated using micron-sized polystyrene latex particles. The improvement of particle throughput by laser scanning was confirmed through a separation experiment using a mixture of micron-sized synthetic diamond and graphite particles. The results showed that the optimized laser beam scan system enables particle separation throughput to be increased by approximately 70% compared to the non-scanning state.