We develop a reduced-order model for large-scale unsteadiness (vortex shedding) in a two-dimensional diffuser and use the model to show how periodic mass injection near the separation point reduces stagnation pressure loss. The model estimates the characteristic frequency of vortex shedding and stagnation pressure loss by accounting for the accumulated circulation due to the vorticity flux into the separated region. The stagnation pressure loss consists of two parts: a steady part associated with the time-averaged static pressure distribution on the wall, and an unsteady part caused by vortex shedding. To validate the model, we perform numerical simulations of compressible unsteady laminar diffuser flows in two dimensions. The model and simulation show good agreement as we vary the Mach number and the area ratio of the diffuser. To investigate the effects of periodic mass injection near the separation point, we also perform simulations over a range of the injection frequencies. Periodic mass injection causes vortices to be pinched off with a smaller size as observed in experiments. Consequently, their convective velocity is increased, absorption of circulation from the wall is enhanced, and the reattached point is shifted upstream. Thus, in accordance with the model, the stagnation pressure loss, particularly the unsteady part, is substantially reduced even though the separation point is nearly unchanged. This study helps explain experimental results of separation control using unsteady mass injection in diffusers and on airfoils.