The Canary Islands are an Atlantic archipelago known for its high number of endemic species. Among the most known endemic vertebrate species are the giant lizards of the genus Gallotia. We describe the cranial osteology of the first almost complete and articulated fossil skull of the taxon Gallotia auaritae, recovered from the lower-middle Pleistocene of the La Palma island. In this work, X-ray computed microtomography images were used to perform an exhaustive phylogenetic analysis where most of the extant and fossil species of the genus Gallotia were included for first time. This analysis recovered a monophyletic Gallotia clade with similar topology to that of molecular analyses. The newly described specimen shares some characters with the group formed by G. bravoana, G. intermedia and G. simonyi, G. auaritae, and its position is compatible with a referral to the latter. Our study adds new important data to the poorly known cranial morphology of G. auaritae, and the phylogenetic analysis reveals an unexpected power of resolution to obtain a morphology-based phylogeny for the genus Gallotia, for inferring the phylogenetic position of extinct species and for helping in the identification of fossil specimens.