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 using several benchmarks.