Proton exchange membrane fuel cell(PEMFC) is widely recognized as a potentially renewable and green energy source based on hydrogen. Maximum power point tracking(MPPT) is one of the most important working conditions to be considered. In order to improve the performance such as convergence and robustness under disturbance and uncertainty,a fractional order high pass filter(FOHPF) is applied for the MPPT controller design based on the traditional extremum seeking control(ESC). The controller is designed with integerorder integrator(IO-I) and low pass filter(IO-LPF) together with fractional order high pass filter(FOHPF), by substituting the normal HPF in the original ESC system. With this FOHPF ESC,better convergence and smoother performance are achieved while maintaining the robust specifications. First, tracking stability is discussed under the commensurate-order condition. Then,simulation results are included to validate the proposed new FOHPF ESC scheme under disturbance. Finally, comparison results between FOHPF ESC and the traditional ESC method are also provided. Proton exchange membrane fuel cell (PEMFC) is widely recognized as a potentially renewable and green energy source based on hydrogen. Maximum power point tracking (MPPT) is one of the most important working conditions to be considered. In order to improve the performance such as as convergence and robustness under disturbance and uncertainty, a fractional order high pass filter (FOHPF) is applied for the MPPT controller design based on the traditional extremum seeking control (ESC). The controller is designed with integerorder integrator (IO-I) and low pass filter (IO-LPF) together with fractional order high pass filter (FOHPF), by substituting the normal HPF in the original ESC system. With this FOHPF ESC, better convergence and smoother performance are maintained while the robust specifications. Then, the simulation results are included to validate the proposed new FOHPF ESC scheme under disturbance. Finally, com parison results between FOHPF ESC and the traditional ESC method are also provided.