In this paper, control of small PEM(Proton Exchange Membrane) fuel cell stack by a microprocessor is introduced. The water management of fuel cell stack inside, a key technique in fuel cell control, can be achieved by adjusting the required air flow for fuel and cooling, and by purging the excessive water from the stack. It is very important to precisely control the BOS(Balance of Stack) since the stable operation of the fuel cell system mainly depends on it. In this study the fuel efficiency of the system is improved by the control of the system based on the measured air flow and purge cycle during the optimal operation and its effectiveness is proved by the experiments. The operating stability of the system is improved by the developed controller using a microprocessor and it is expected to be widely used for the control of small PEM fuel cell stack.