Modeling and control of proton-exchange membrane fuel cells (PEMFC) has become a very popular research topic lately due to the increasing use of renewable energy. Despite this fact, most of the work in the current literature only studies standard dynamical models without taking into consideration possible parasitics such as small gas flow perturbations that could be available in the system. This paper addresses this issue by elaborating on time-scale modeling of an augmented eighteenth-order PEMFC-reformer system via singular perturbation theory. The latter captures time scales that arise in the model due to the presence of small perturbations. Specifically, a novel and efficient algorithm that helps identify the presence of different time-scales is developed. In addition, the method converts an implicit singularly perturbed model into an explicit equivalent where the time-scales are evident. Using this algorithm, a complete singularly perturbed dynamic model of the augmented eighteenth-order PEMFC-reformer system is obtained. Modeling of the PEMFC-reformer system is followed by linear quadratic regulator (LQR) design for the individual time-scales present in the system.