Fuel cell powered vehicles are comparatively more efficient than conventional vehicles which utilise fossil fuel as a main fuel source for energy conversion. This paper discusses Harmony Search optimized Fractional Order Proportional Integral Derivative (HS-FPID) controller which is used to regulate the speed of the Proton Exchange Membrane Fuel Cell (PEMFC) powered vehicle. The robust and the swift response of the HS-FPID controller makes it superior to other existing controllers and hence it is also utilized to control the DC Motor speed of PEMFC powered vehicles. The robustness and the swiftness of the HS-FPID controller is established using MATLAB Simulink.