This paper presents a Proton-Exchange Membrane Fuel Cell (PEMFC) transient model in stack current cycling conditions and its partial optimal control. The derived model is used for a specific application of the recently published multistage control technique developed by the authors. The presented control-oriented transient PEMFC model is an extension of the steady-state control-oriented model previously established by the authors. The new model is experimentally validated for transient operating conditions on the Greenlight Innovation G60 testing station where the comparison of the experimental and simulation results is presented. The derived five-state nonlinear control-oriented model is linearized, and three clusters of eigenvalues can be clearly identified. This specific feature of the linearized model is known as the three timescale system. A novel multistage optimal control technique is particularly suitable for this class of systems. It is shown that this control technique enables the designer to construct a local LQR, pole-placement or any other linear controller type at the subsystem level completely independently, which further optimizes the performance of the whole non-decoupled system.