Improper humidification of reactant gasses and operating with non optimal temperature values are main factors influencing fast degradation of the most expensive element of PEM fuel cell stack, i.e. polymer electrolyte membrane. The thermal subsystem keeps fuel cell stack temperature at desired level to achieve optimal conditions of fuel cell operation . The humidification subsystem ensures the ionic conduction which is a basic element of working the PEM. Since water as a by-product of the fuel cell is an element used in both subsystems whereas heat supports a humidification process, both subsystem were integrated. The paper focuses on modeling and implementation of the both subsystems of 6 kW PEM fuel cell stack. In the first chapter of the paper, a mathematical model of the thermal subsystem is presented. Then, a selection of the thermal and humidification subsystems elements were considered. At the end of the paper, conclusions are included and further researches are shortly presented.