Precise knowledge of the timing of deformation in the Subandean zone of the Andean Plateau is a prerequisite for deciphering the late Neogene growth of the Andean Plateau. In this paper, we report new apatite fission-track (AFT) and vitrinite reflectance (Ro) data for a regional balanced cross section of the Camisea Basin in the central Peruvian Subandean zone, adjacent to the northern Andean Plateau. The balanced cross section shows that the structure of this basin is characterized by a broad internal passive roof duplex and external thrust- related anticlines. The balanced cross-section restoration shows 53 km (39%) of total horizontal shortening. We sampled Paleozoic to Cenozoic sedimentary strata for AFT and Ro analyses along the ∼4-km-thick vertical profile of the Mainique back thrust (passive roof thrust), the innermost preserved Subandean structure. Young components of AFT ages are spread between ca. 6 Ma and ca. 24 Ma. A break in the slope in the AFT ages determines the geometry of the Miocene partial annealing zone and the exhumation of the Mainique back thrust at ca. 6 Ma. Sequential restoration calibrated by AFT and Ro data indicates that the last ∼23 km horizontal shortening were accommodated by the Camisea thrust system over the past ∼6 m.y., giving a mean shortening rate of 3.8 mm/yr. Using this shortening rate for the first ∼30 km horizontal shortening, we calculate that the Andean shortening transfer into the Peruvian Subandean zone initially started at ca. 14 Ma. This result suggests that the transfer of shortening from the northern Andean Plateau to the Subandean zone occurred prior to the removal of dense lithosphere previously reported to have occurred between ca. 10 Ma and ca. 7 Ma. We rather propose that the late Neogene growth of the northern Andean Plateau mostly resulted from a continuous crustal shortening combined with lower-crustal flow.