This article describes the development and testing of a modified, semi-empirical ONERA dynamic stall model for an airfoil with a trailing edge flap—a “smart airfoil”—pitching at reduced frequencies up to 0.1. The Reynolds number is 105. The model reconstructs the load fluctuations associated with the shedding of multiple dynamic stall vortices (DSVs) in a time-marching solution, which makes it suitable for real-time control of a trailing edge flap (TEF). No other model captures the effect of the DSVs on the aerodynamic loads on smart airfoils. The model was refined and tuned for force measurements on a smart NACA 643-618 airfoil model that was pitching with an inactive TEF and was validated against the measurements when the TEF was activated. A substantial laminar separation bubble can develop on this airfoil, which is challenging for modelers of the unsteady response. A closed-loop controller was designed offline in SIMULINK, and the output of the controller was applied to the TEF in a wind tunnel. The results indicated that the model has a comparable accuracy for predicting loads with the active TEF compared to inactive TEF loads. In the fully separated flow regime, the controller performed worse when dealing with the development of the laminar separation bubble and DSVs.