Active control of flow separation was conducted with active vortex generator and micro flow sensor. The sensor can detect the momentum transport. Since the static characteristics of the sensor output has the near wall velocity corresponding to an extremum, it is possible to implement the maximization of the transport by using so-called extremum seeking and slope-seeking control. The input of the plant in the control system is an angle of attack of vortex generator and the output is the sensor output. As a result of applying the system to flow separation upstream of fence in the turbulent boundary layer, we confirmed the effectiveness of the system including the dynamic response.