The synchronous application of flow control in the presence of unsteady wakes was studied on a highly loaded low pressure turbine blade. At low Reynolds numbers, the blade exhibits a nonreattaching separation bubble under steady flow conditions without upstream wakes. Unsteady wakes from an upstream vane row are simulated with a moving row of bars. The separation zone is modified substantially by the presence of unsteady wakes, producing a smaller separation zone and reducing the area-averaged wake total pressure loss by more than 50%. The wake disturbance accelerates transition in the separated shear layer but stops short of reattaching the flow. Rather, a new time-averaged equilibrium location is established for the separated shear layer. The focus of this study was the application of pulsed flow control using two spanwise rows of discrete vortex generator jets. The jets were located at 59% , approximately the peak location, and at 72% . The most effective separation control was achieved at the upstream location. The wake total pressure loss decreased 60% from the wake-only level and the distribution fully recovered its high Reynolds number shape. The jet disturbance dominates the dynamics of the separated shear layer, with the wake disturbance assuming a secondary role only. When the pulsed jet actuation was initiated at the downstream location, synchronizing the jet to actuate between wake events was key to producing the most effective separation control. Evidence suggests that flow control using vortex generator jets (VGJs) will be effective in the highly unsteady low pressure turbine environment of an operating gas turbine, provided the VGJ location and amplitude are adapted for the specific blade profile.