Microfluidic biochips are replacing the conventional biochemical analyzers integrating the necessary functions on-chip. We are interested in flow-based biochips, where a continuous flow of liquid is manipulated using integrated microvalves, controlled from external pressure sources via off-chip control pins. Recent research has addressed the physical design of such biochips. However, such research has so far ignored the pin-count, which rises with the increase in the number of microvalves. Given a biochip architecture and a biochemical application, we propose an algorithm for reducing the number of control pins required to run the application. The proposed algorithm has been evaluated on several biochips, including the AquaFlux biochip from Microfluidic Innovations LLC.