The uplift processes of the Qilian Shan (northern Tibetan Plateau) play a central role in our understanding of the dynamics of outward and upward growth of Tibet due to sustained convergence of the Indian and Asian plates. We employ apatite fission track chronology and geological mapping to reveal the time and pattern of the deformation along the Qilian Shan. Our results indicate that the emergence of the Tuolai Shan in the central Qilian Shan occurred at 17–14 Ma, that northern Qilian Shan thrusting began at 10–8 Ma, and that the Laojunmiao anticline formed ca. 3.6 Ma. Together with previous results that show that uplift of the southern Qilian Shan began in the Oligocene, we suggest that the Qilian Shan has undergone progressively northward expansion in the Cenozoic due to significant crustal shortening driven by Qilian Shan thrust fault systems.