The present invention relates to an afterbody flow control system and more particularly to aircraft or missile flow control system for enhanced maneuverability and stabilization. The present invention further relates to a method of operating the flow control system.In one embodiment, the present invention includes a missile or aircraft comprising an afterbody and a forebody; at least one activatable flow effector on the missile or aircraft afterbody; at least one sensor each having a signal, the at least one sensor being positioned to detect forces or flow conditions on the missile or aircraft afterbody; and a closed loop control system; wherein the closed loop control system is used for activating and deactivating the at least one activatable flow effector based on at least in part the signal of the at least one sensor.