A purification system and method for purifying a hydrogen stream supplied from a storage tank mounted in a vehicle to produce a purified hydrogen stream for use in a PEM fuel cell system that is utilized within the vehicle. The hydrogen is purified within a membrane separator having hydrogen transport membrane elements having a dense metallic layer such as palladium to separate the hydrogen from the impurities. The separated hydrogen is supplied to the PEM fuel cell. In order to heat the membrane to its operational temperature, heat is recovered from the hydrogen permeate stream of the membrane system in a first heat exchanger and heat is generated by combusting the retentate stream containing residual hydrogen and impurities.