A fluorescence-activated particle counting and sorting system is developed for lab-on-a-chip applications. This system integrates the microfluidic chip, fluorescence excitation and detection, electronic power switch control, and optical visualization. The automatic sorting function is achieved by electrokinetic flow switching, which is triggered by a pre-set fluorescent threshold. A direct current electric pulse is generated to dispense the fluorescent particles to the collection reservoir. A user-friendly software interface is developed for automatic real-time counting, sorting and visualization. The design of the disposable microfluidic chip is simple and easy for integration. This system represents a promising prototype for development of affordable and portable flow cytometric instruments.