Backstripped tectonic basin subsidence histories are critical for interpreting phases of lithospheric deformation and paleoenvironmental change from the stratigraphic record. This study presents new subsidence modeling of the Rocas Verdes Backarc Basin (RVB) and Magallanes-Austral retroarc foreland basin (MAB) of southernmost South America to evaluate along-strike changes in tectonic subsidence related to the Late Jurassic through Miocene history of the Southern Andes. We compiled composite stratigraphic sections for seven basin localities that span 47°–54°S from published sedimentological records of paleoenvironment, paleobathymetry, and geochronology. Modeling results resolve regional trends in basin tectonic subsidence, uplift, and sedimentation rate that influenced the depositional environment during five broad phases of RVB-MAB development: (a) Late Jurassic tectonic subsidence and basin deepening associated with rift-related backarc extension that postdated regional diachronous rift-related magmatism. (b) Southward younging of Early to Late Cretaceous pronounced acceleration in tectonic subsidence interpreted as the initiation of flexural loading and development of the MAB foreland basin system. (c) Late Cretaceous (ca. 85–70 Ma) tectonic uplift within the central foredeep ∼49° to 52°S, coeval with a shift from slope to shelf deposition at these latitudes. (d) A protracted period of low-magnitude basin uplift and relative tectonic quiescence during the Paleogene, with the exception of southernmost localities; and (e) Synchronous latest Oligocene-early Miocene tectonic subsidence linked to basin deepening and transgression across the northern and central basin sectors. Backstripped tectonic subsidence analysis corroborates existing interpretations for orogenic development in the RVB-MAB and sheds new light on complex polyphase basin histories where extension precedes convergence.