Missiles suffer from flight instability problems at high angles of attack, since vortex flow over a fuselage cause lateral force to the body. To overcome this problem at a high angle of attack, the development of a real time vortex controller is needed. In this paper, Proper Orthogonal Decomposition (POD) and feedback controllers are developed for real time vortex control. The POD method is one of the most well known techniques for modeling low order models that represent the original full-order model. An adaptive control algorithm is used for real time control.