A mathematical model is developed to predict the effect of flow separation on the unsteady aerodynamic lift and moment acting on an harmonically oscillating two-dimensional airfoil in a subsonic flow field. The unsteady flow is considered to be a small perturbation to the uniform steady flow, with the steady flow assumed to separate at a specified fixed position on the airfoil suction surface. This formulation does not require the difference in the upwash velocity across the airfoil in the separated flow region to be determined before calculating the unsteady pressure difference across the airfoil chordline, thereby eliminating the assumption that the upwash difference is zero at the trailing edge when the steady flow is separated. This model is then used to demonstrate the effects of flow separation on the unsteady aerodynamics of an oscillating airfoil.