Micro air vehicles (MAV) are a major focus of aerodynamics today with many military as well as civilian applications. MAV flight is dominated by the unsteady characteristics of low Reynolds number flows. Three-dimensional separations may occur at random on different parts of the wing, causing highly unsteady forces and moments, as well as full wing stall. In the present work an Electro-Active Polymer (EAP) actuator was examined as a feasible flow control actuator with application to low Reynolds number flows. The performance of the EAP was evaluated using a laser displacement device, where the displacements generated under selected driving frequencies and input voltages were recorded. It was shown that the deflections could reach up to 0.35 mm at frequencies below 40 Hz. The surface deflection was found to be parabolic across the span and width of the actuator. Hot-wire anemometry measurements were conducted on a flat plate equipped with a trailing edge flap in a low Reynolds number wind tunnel to study the effects of the EAP on a transitional boundary layer. Two actuation frequencies were chosen, corresponding to the Tollmien-Schlichting waves of the boundary layer and the Kelvin-Helmholtz waves (due to the presence of an inflection point). The actuation at a frequency corresponding to the inflection point was found to be the most effective in altering the boundary layer as well as its turbulence intensities.