A tectonic model for the formation, subsidence, and thermal history of Queen Charlotte Basin is developed. Based upon regional geological and geophysical data, subsidence data from offshore wells in Hecate Strait and Queen Charlotte Sound, and thermal criteria derived from present heat flow and vitrinite reflectance information, Queen Charlotte Basin is seen to have resulted from two distinct mechanisms. (1) During a period of broad regional uplift, rifting and crustal extension occurred in Queen Charlotte Sound up to about 17 Ma ago and the Queen Charlotte Islands were displaced northwards toward their present position by transcurrent motion along the Louscoone Inlet – Sandspit fault system. The rifting generated a significant thermal anomaly and a restricted deep basin as a consequence of crustal thinning and subsequent thermal cooling. (2) Beginning about 6 Ma ago, oblique underthrusting commenced along the margin, resulting in flexural uplift of the western part of the Queen Charlotte Islands and companion subsidence in Hecate Strait and Queen Charlotte Sound. The underthrusting caused rapid cooling of the old rift basins. This phase of subsidence has continued at a decreasing rate until the present.The tectonically generated subsidence in the basin has been estimated by correcting the well data for sediment compaction, paleo water depth, and sediment loading effects. At the site of the Harlequin well in the Queen Charlotte Sound rift, with the termination of extension and associated volcanism, the basin was 1500–2000 m deep and contained little sediment. Model calculations show that this depth is consistent with the estimated extension of about 70 km and a resulting crustal thinning to 8–10 km.Models for the lithosphere flexure generated by underthrusting are constrained by the geological evidence for uplift and erosion of over 5 km of material from the western portion of the Queen Charlotte Islands and the exponentially slowing subsidence to a present regional basement depth of 2 km in Hecate Strait. An excellent fit to the pre-erosion surface profile onshore and pre-Skonun basement surface offshore is obtained with a model having underthrusting on a 30° thrust at a 10 mm year−1 orthogonal component of convergence. The flexure generated by underthrusting, which is particularly well documented in the Queen Charlotte region, appears to be a feature of most subduction zones.Vitrinite reflectance data, present heat flow estimates from the wells, and thermal modelling indicate that the heat flux in Queen Charlotte Basin was much higher in the past than at present, particularly in Queen Charlotte Sound. A model is proposed with high heat flow generated by rifting prior to 17 Ma ago, followed by cooling from the underthrust oceanic lithosphere.