The Cenozoic intramontane Gonghe–Guide Basin in Qinghai Province, China, is tectonically controlled by the sinistral strike-slip framework of the Kunlun and Altyn Tagh–South Qilian faults in the northeastern Tibetan Plateau. The basin is filled with thick Cenozoic clastic sedimentary formations, which provide important evidence of the deformation of this part of the plateau, although they have long lacked good age constraints. Detailed magnetostratigraphic and paleontologic investigations of five sections in the Guide Basin and their lithologic and sedimentary characteristics allow us to divide a formerly undifferentiated unit (the Guide Group) into six formations (where ages are now magnetostratigraphically well established, they are given in parentheses): the Amigang (1.8–2.6 Ma), Ganjia (2.6–3.6 Ma), and Herjia formations (3.6 to ca. 7.0–7.8 Ma), and the older Miocene Ashigong, Garang, and Guidemen formations. These rocks document a generally upward coarsening sequence, characterized by increasing accumulation rates. Increasing gravel content and sizes of its components, changes of bedding dips and source rock types, and marginal growth faults collectively reflect accelerated deformation and uplift of the NE Tibetan Plateau after 8 Ma, punctuated by a sharp increase in sedimentation rate at ca. 3.2 Ma that reflects the boulder conglomerates of the Ganjia formation. Interestingly, much of the vergence of the compressional deformation in the basin is to the south, accommodated by a sequence of six thrusts (F1–F6), which become active one by one progressively later toward the south, undoubtedly contributing to the uplift of this part of the plateau. F1 likely initiated the Guide Basin due to crustal flexure in the Oligocene, F2 was active in the early Miocene, F4 and F5 at ca. 3.6 Ma, and F6 was active in the early Pleistocene. The detailed late Miocene and younger magnetostratigraphy allows us to place much improved time constraints on the deformation and, hence, uplift of northeastern Tibet, which, when compared with ages for events on other parts of the plateau, provides important boundary conditions for the geodynamical evolution of Tibet.