A deep seismic reflection transect and coincident refraction study reveal the crustal structure developed during Mesoproterozoic orogenesis preserved in the Mount Isa inlier of northwest Queensland, Australia. Geologic interpretation of the reflection data indicates a two-stage evolution for east-west shortening. The first stage involved west-directed folding and thrusting above a decollement in the eastern part of the terrane. This decollement system was the forehand of an orogenic system rooted east of the present day inlier. The second stage is characterized by a network of basement-cutting reverse and strike-slip faults that dissected the decollement. This overprinting system was linked to crustal thickening within the Mount Isa terrane.The refraction profile indicates the crust beneath the inlier is currently approximately 55 km thick. Rocks with transitional velocities >7 km/s in the lower 15 km are interpreted as mafic underplate formed during the pre-orogenic rift history of the inlier. The refraction profile also reveals two west-dipping, high-velocity layers within the crust. Evaluating the origin of these layers in light of the kinematics of crustal thickening suggests they are portions of the underplated material thrust to midcrustal levels during the second stage of shortening. The overprinting orogenic scenario has implications for the geodynamic evolution of the inlier that should have a direct bearing on mineralizing systems localized by reverse faults developed during the second stage of shortening. This basement-cutting stage established a linked fault network able to tap deeper crustal circulation during the intrusion of late to postorogenic granitoids.