Frequency effects of the synthetic jet on the flow field over a backward facing step are investigated using numerical analysis. Three-dimensional Navier-Stokes equations are solved. Implicit large-eddy simulation using high-order compact difference scheme is conducted. The present analysis is addressed on the frequency characteristics of the synthetic jet for understanding frequency characteristics and flow filed. Three cases are analyzed; the case computing flow over backward facing step without control, the case computing flow with synthetic jet control at F+h =0.2, and the case computing flow with synthetic jet control at F +h =2.0, where non-dimensional frequency F +h is normalized with the height of backward-facing step and the freestream velocity. The present computation shows that separation length in the case of the flow controlled at F+h =0.2 is 20 percent shorter than the case without control. Strong two-dimensional vortices generated from the synthetic jet interact with the shear layer, which results in the increase of the Reynolds stress in the shear layer region. These vortices are deformed into three-dimensional structures, which make Reynolds stress stronger in the recirculation region. Size of the separation length in the case of the flow controlled at F+h =2.0 is almost the same as the case without control because the mixing between the synthetic jet and the shear layer is not enhanced. Weak and short periodic vortices induced from the synthetic jet do not interacts with the shear layer very much and diffuse in the recirculation region.