Numerous extensional faults offset the passive margin strata of the northern Bonaparte Basin. This extensional deformation has been attributed to lithospheric flexure of the descending Australian Plate, in an overall convergence setting. Here we use an extensive 2D and 3D seismic dataset calibrated with well biostratigraphy and strontium (Sr) isotope age data to constrain the timing of deformation along the northern Australian margin during the Neogene. Analysis of fault throw and differential thickness variations give new insights on the propagation and slip history of the faults. Along-dip throw profiles exhibit ‘D’ shape distributions, skewed towards the top. Positive throw gradients above the throw maxima, coinciding with intervals of growth strata, indicate multiphase fault activity. Results indicate that post-rift extensional deformation initiated during the latest Miocene (ca. 6 Ma). The development of the modern Timor Trough (as a foreland basin) and Cartier Trough also commenced during this period. A second episode of increased tectonic activity occurred around the Pliocene–Quaternary boundary (ca. 3 Ma), and the deformation continued intermittently to the present-day. These new results are in agreement with the timing of initiation of collision between the Australian Plate and the Banda Arc and uplift of the Timor Island, recently derived from stratigraphic analysis in Timor. These regional tectonic events have profoundly affected the paleogeography of the Timor Sea and may explain major changes in oceanic circulation and climate during the Neogene.