This paper discusses the physical dynamics of the use of the Active Flow Control (AFC) actuators embedded in a Vertical Take-Off and Landing (VTOL) aircraft. Results of High-Fidelity numerical simulations are examined at near stall conditions. Different approaches of AFC are proposed to suppress the flow separation at these conditions. First the flow around the VTOL aircraft at high angle of attack in the take-off and landing configurations in real flight conditions at high Reynolds number are examined, then different flow control strategies are investigated. It was found that at these flow condition a flow separation travels along the spanwise direction in the near trailing-edge region of the wing with additional corner vortices between the wing-nacelle and the wing-fuselage junctions. Zero Net Mass Flux (ZNMF) actuators, also called synthetic jets, were then used for Active Flow Control. It was found that these ZNMF devices, when operating at the optimal blowing velocity and activation frequency, and when placed at the correct location enable the flow to re-attach and to delay the flow separation, resulting in an increase in aerodynamic efficiency of the aircraft. This work presented in this paper has been carried out in the context of the European project CleanSky2 Active Flow Control for TiltRotor aircraft (AFC4TR), Grant Agreement 886718.