Autothermal reactors, coupling endothermic and exothermic reactions in parallel channels, represent one of the most promising technologies for hydrogen production. The bulk of existing research work concerning their operation refers, however, to steady-state conditions. In the present work, we analyze the dynamic behavior of autothermal reactors. We demonstrate that such systems are modeled by systems of equations that are stiff, their dynamics consequently featuring two time scales. Within the framework of singular perturbations, we derive reduced-order, non-stiff models for the transient evolution in each time scale, and draw an analogy between the rigorously derived model of the slow dynamics and widely-accepted empirical low order models used in the literature. Furthermore, we uncover some of the challenges posed by the transient operation of autothermal reactors, and demonstrate the implementation of feedback control to improve transient performance. All theoretical concepts are illustrated with numerical simulations performed using the model of a hydrogen production reactor.