We use two-plane-wave tomography with a dense network of seismic stations across Sabah, northern Borneo, to image the shear wave velocity structure of the crust and upper mantle. Our model is used to estimate crustal thickness and the depth of the lithosphere-asthenosphere boundary (LAB) beneath the region. Calculated crustal thickness ranges between 25 and 55 km and suggests extension in a NW-SE direction, presumably due to back-arc processes associated with subduction of the Celebes Sea. We estimate the β-factor to be 1.3–2, well below the initiation of seafloor spreading. The LAB is, on average, at a depth of 100 km, which is inconsistent with models that ascribe Neogene uplift to wholescale removal of the mantle lithosphere. Instead, beneath a region of Plio-Pleistocene volcanism in the southeast, we image a region 50–100 km across where the lithosphere has thinned to <50 km, supporting recent suggestions of lower lithospheric removal through a Rayleigh-Taylor instability.