This paper presents a Proton Exchange Membrane Fuel Cell (PEMFC) system model for locomotives, implemented ad hoc in MATLAB-Simulink environment for a standard drive cycle; the system is hybrid and the energy store system (ESS) is composed of battery and supercapacitor (SC). The PEMFC is the primary energy source of the hybrid locomotive; it supplies the total energy demand. A battery supplies the additional energy demand in acceleration and the SC delivers the power to fill the peaks. Moreover, a regenerative brake recuperates part of the energy lost in deceleration and stores it in the ESS. The hybrid locomotive is controlled by a hybrid strategy, fit for the purpose, composed of Fuzzy Logic Control and Equivalent Consumption Minimization Strategy; the PEMFC power is obtained through an optimization problem and the other variables are calculated by means of IF-THEN rules in order to achieve best results from each energy source, high efficiency and low hydrogen consumption. The simulation results confirm the good response of the hybrid system model: the FC system achieves efficiency of around 50% with a hydrogen consumption of 1.3 kg; the battery State of Charge (SOC) is kept between 60% and 75% and the SC SOC between 30% and 90%.