In response to the industrial needs for automated handling of very thin solar cell wafers, this paper presents the design concept for the individual wafer separation from the stacked wafers by utilizing continuous water jet. The experimental apparatus for automated wafer separation was constructed and it includes the water jet system and the microprocessor controlled wafer stack advancing system. Through a series of tests, the performance of the proposed design is quantified into the success rate of single wafer separation and the rapidity of processing wafer stack. Also, the inclination angle of wafer equipped cartridge and the water jet flowrate are found to be important parameters to be considered for process optimization. The proposed design shows the concept for fast and efficient processing of wafer separation and can be implemented in the automated manufacturing of silicon based solar cell wafers.