In this study we investigate simulate the heat transfer enhancement behind a backward facing step with active flow control. The numerical simulations are carried out by a finite volume based laminar, incompressible, unsteady flow solver (ANSYS-Fluent) in a two-dimensional computational domain with Cartesian cells including a moving zone to mimic the periodic motion of the actuator plate. The active flow control device used is a Jet and Vortex Actuator (JaVA) that is shown previously to delay or prevent flow separation. JaVA in its simple form is a rectangular cavity containing an asymmetrically located plate on its opening which moves in horizontal direction with a certain amplitude and frequency. Depending on the motion of the plate, fluid is either ejected out of the cavity or sucked into the cavity. The jet or vortex ejected downstream of the backward facing step transport momentum to the base flow, increases the mixing and thus enhancing heat transfer. Keeping the amplitude and the plate width constant for all cases, it is observed that with increasing frequency (jet-Reynolds number), the traveling vortical structures form downstream of the channel. These vortical structures significantly increase the rate of heat transfer due to better mixing. It is reported that the forming vortical structures in channel is the main mechanism for the increase of heat transfer. It is found that as the incoming flow Reynolds number increases, the extent of the traveling vortical structures moves far downstream distances and the Nu values are much higher compared to the non-actuated base flow.