Our previous research has shown that an effective and efficient laminar separation control is achieved when an inviscid shear-layer instability is exploited. How such active flow control strategies are affected by free-stream turbulence remains an open question. To address this question, highly resolved direct numerical simulations were carried out where isotropic turbulence was introduced at the inflow boundary. Without control, the length of the separated region was reduced when the free-stream turbulence intensity was increased. For a free-stream turbulence intensity of 3%, detailed investigations of active flow control using pulsed vortex generator jets (PVGJs) were carried out. The spanwise jet spacing, the blowing ratio, and the actuation frequency were varied. The present results indicate a clear optimum for all three parameters. A detailed analysis of the simulation data based on Fourier transforms, proper orthogonal decomposition, and instantaneous flow visualizations was carried out to provide detailed insight into the time-dependent fluid dynamics. Particular emphasis was placed on the downstream evolution of the disturbance Fourier mode amplitudes which provide indications for possible flow instabilities.