The Taranaki Basin contains most of New Zealand’s commercial hydrocarbon reserves. The southern parts of Taranaki Basin underwent inversion during the late Miocene, with published AFTA and vitrinite reflectance data suggesting ~2.5 to 3 km of section eroded from the structure on which the Fresne-1 well was drilled, consistent with estimates from reconstructions based on seismic sections. The well-constrained tectonic and thermal history framework for this well-section, established by earlier studies, provides an ideal test-bed for the thermochronological technique of apatite (U-Th)/He dating. Helium ages determined in apatites from the earlier AFTA study decrease from ~6 Ma at ~400 metres depth to ~1 Ma at 2465 metres. While these results are qualitatively consistent with Late Miocene cooling, quantitative modelling of (U-Th)/He ages based on best-fit thermal histories derived from new AFTA analyses (using improved methods) suggests that cooling was protracted, involving accelerated cooling during the Pliocene possibly indicating a discrete Pliocene inversion phase. Integration of AFTA and (U-Th)/He dating can provide improved thermal history constraints in sedimentary basins, particularly on cooling rates and/or resolution of multiple thermal events. By independently defining the timing of peak maturation in relation to formation of potential trapping structures, this information offers the potential for improved assessment of hydrocarbon prospectivity and reduced exploration risk.