Cenozoic sedimentary rocks of the intermontane Bagua Basin record the Andean orogenic history of northern Peru at ~4–7°S. The northern Peruvian Andes define the northern termination of the Central Andes and are comprised of a narrow, low-elevation orogen relative to the rest of the Central Andes. New stratigraphic and sedimentologic field observations, subsidence analysis, and detrital zircon provenance analysis enable reconstruction of the regional tectonic history. Late Cretaceous to Paleocene detrital zircon U-Pb age spectra from the Fundo El Triunfo and Rentema formations reveal active volcanism in the Western Cordillera as early as ~80 Ma and early exhumation of Mesozoic rocks in a nascent Marañon Fold-Thrust Belt. Eocene fluvial deposits of the Cajaruro Formation record a progressive increase in shortening and volcanism in the Western Cordillera. The upper Eocene–middle Miocene fluvial succession of the Sambimera Formation records deposition in a proximal foredeep setting. Sambimera deposits contain syndepositional detrital zircon U-Pb age populations that reveal a major Cenozoic magmatic source in the west. An erosive boundary separates the Sambimera from the overlying San Antonio Formation. The San Antonio Formation was deposited in an intermontane basin associated with uplift of the Eastern Cordillera at these latitudes. These results highlight a foreland progression of fold-thrust deformation, with shortening concentrated in the Western Cordillera from latest Cretaceous to middle Miocene time. We suggest that the late Miocene transition to intermontane deposition in the Bagua Basin marks initial exhumation during shortening of the Eastern Cordillera in northern Peru.