The kinematic evolution of the West Antarctic rift system has important consequences for regional and global geodynamics. However, due to the lack of Neogene seafloor spreading at the plate boundary and despite being poorly resolved, East-West Antarctic motion was assumed to have ended abruptly at 26 million years ago. Here we present marine magnetic data collected near the northern edge of the rift system showing that motion between East and West Antarctica lasted until the middle Neogene (~11 million years ago), long after the cessation of the known mid-Cenozoic pulse of motion. We calculate new rotation parameters for the early Neogene that provide the kinematic framework to understand the varied lithospheric settings of the Transantarctic Mountains and the tectono-volcanic activity within the rift. Incorporation of the Antarctic plate motion into the global plate circuit has major implications for the predicted Neogene motion of the Pacific Plate relative to the rest of the plates.