The efficiency of the fuel cell system nonlinearly depends on operating conditions and the air flow supplied to the fuel cell system is one of the most significant factors in determining the efficiency. The conventional method of controlling the air flow is to stabilize the oxygen supply at a predetermined constant rate for the optimal efficiency. However, in practice, the optimal point can deviate from the pre-set value due to the varying operating conditions, such as the uncontrollable load. Therefore, the maximum efficiency point tracking (MEPT) controller is necessary to maintain the optimal efficiency over a broad range of operating conditions. In this paper, the MEPT controller is designed based on the extremum seeking control algorithm for searching the optimal oxygen excess ratio in real time to maximize the efficiency of the fuel cell system. Simulation was conducted in the MATLAB/SIMULINK environment and the results demonstrate that the proposed control method is able to track the maximum efficiency point when variations in operating conditions occur.