The paucity of Phanerozoic rock sequences in the Proterozoic Mt Isa and Murphy Inliers in northern Australia renders it difficult to determine their Phanerozoic tectonic histories. However, thermochronological methods provide a means to assess this problem. Apatite fission track ages vary from 390 to 218 Ma, and mean track lengths range between 11.1 and 13.6 μm. These results record a non-linear cooling history below about 110 ± 10°C. Forward modelling of the fission track data suggests that the first episode of relatively rapid cooling since the Early Carboniferous occurred between ca 350 and 250 Ma at rates of ∼0.9°C/million years and was synchronous with intracontinental deformation associated with the Alice Springs Orogeny and tectonics at the contemporaneous eastern margin of Australia. This event resulted in ≥ 2 km of exhumation across both inliers. Cooling rates also increased after 100 Ma, although estimates of the amount of cooling and exhumation across trhe inliers obtained by forward modelling of the fission track data exceed those determined by constraints provided by the 40Ar/39Ar ages of weathering profiles. This observation adds to the growing amount of evidence that the fission track annealing model employed overestimates cooling rates at low temperatures (<60 – 70°C). The spatial variation of apatite fission track data within the Mt Isa Inlier indicates the three major structural belts, the Western Fold Belt, Kalkadoon – Leichhardt Belt and the Eastern Fold Belt, which are separated by major north – south faults, experienced similar thermal histories on a regional scale. This suggests that the main faults bounding the belts have not experienced major reactivation in a vertical sense, as a single large-scale fault plane, since ca 350 Ma. However, adjacent smaller scale, fault-bounded blocks within the structural belts demonstrate variable cooling histories, suggesting that reactivation of favourably oriented minor faults in the inlier, including segments of the major faults, has occurred over this time interval. Variations in apatite fission track data show that up to 1.5 km of vertical displacement occurred along parts of the Mt Isa Fault Zone and the Pilgrim Fault between 350 and 250 Ma.