The post-subduction tectonic evolution of northern Borneo, which experienced two sequential subduction episodes of opposite polarity in the Neogene, is still widely debated with first-order questions such as whether the region has been in a state of compression or extension remaining unresolved. We use waveform data recorded from a dense seismic network in northern Borneo to investigate crustal thickness variations through the application of Virtual Deep Seismic Sounding (VDSS). The new results reveal an extensive area of thin crust in central and southeastern Sabah that appears to extend northeast into the Sulu Sea, where rifting initiated. We also compute local earthquake focal mechanisms, which suggest that extension is ongoing, though now dominated by orogen collapse in the NW. Together these results point to the pervasiveness of regional extension tectonics over the last 15-20 Myr and its role in the post-subduction cycle of plate tectonics in SE Asia.