The Palawan Pleistocene Aggregate Island Complex, a western Philippines island group, possesses a complex geologic history and numerous endemic vertebrates. On the basis of multiple unique morphological features, bolstered by genetic data supporting divergent lineages, we describe the first Philippine endemic species of Lygosoma from Palawan and Cuyo islands. This new semifossorial species is phenotypically similar to Lygosoma quadrupes, a widespread Southeast Asian scincid lizard. We recognize the Palawan lineage as a new species, the second member of the L. quadrupes species complex, and comment on its ecology and conservation status. This new species increases species-level diversity in the genus to 31, including 19 species distributed across Southeast Asia.