The pulsed jet is a novel and effective active mixing enhancement approach. For the transverse pulsed jet in the supersonic crossflow, the frequency influence is investigated using the three-dimensional Reynolds-averaged Navier–Stokes (RANS) equations coupled with the SST k-ω turbulence model. The averaged flow field properties of the pulsed jet are better than those of the steady jet when considering mixing efficiency and jet penetration depth, especially for the case with the pulsed frequency being 50kHz. The flow field structures of the pulsed jet are connected with the time, with periodic wave structures generating in the flow field and moving downstream. The size of the wave structures and its distance are related to the frequency, namely the size and flow distance are relatively small at 50kHz, and it takes some time for the pulsed jet to establish its influence in the full flow field. At low frequencies, the flow field produces large fluctuations, and this may be detrimental to the stable operation of the engine.