Borneo is an island situated in a tectonically complex region and characterised by multiple arcs and continental blocks accreted during the Mesozoic and early Cenozoic. We analyse receiver functions of teleseismic events from 12 seismic stations around the island. In general, these stations sample a variety of geological environments, including Meratus Complex, Eastern Borneo, South–Western Borneo, North–Western Borneo, and Sabah Zones. We then derive the shear wave velocity models from the inversion of receiver functions using the stochastic non-linear approach. Inversion results indicate that the island is covered by sedimentary layers with thickness ranging from 1 to 3 km thick. The inversion solutions for most stations also show that the crustal thickness varies between 26 and 36 km around the region. The variation in the average crustal Vp/Vs values obtained for each seismic station addresses the geological diversity of the study area. Furthermore, the low-velocity zone with high and low Vp/Vs in the lower crust observed beneath some seismic stations may be associated with the tectonic evolution and development of Borneo Island. The results inferred from our inversion are generally consistent with other previous geological and geophysical studies conducted in this region.