Geckos (Gekkota) are a highly diversified group of lizards with an exceptional diversity in sex-determining systems. Despite this intriguing documented variability, data on sex determination in many lineages is still scarce. Here, we document the previously overlooked heteromorphic ZZ/ZW sex chromosomes in the thick-tailed gecko, Underwoodisaurus milii, a member of the ancient lineage of pygopodoid geckos. The finding of female heterogamety within pygopodoid geckos was unexpected, as until now only male heterogamety and environmental sex determination have been reported in this group, and female heterogamety was known only in distantly related gecko families separated from the pygopodoid geckos around 150 million years ago. The W chromosome in U. milii is highly heterochromatic and contains a large number of telomeric-like repeats comparable to around 50% of all telomeric-like sequences present in male genomes. The accumulation of these repeats might have been responsible for the considerable size expansion of the W chromosome in comparison to the Z chromosome. The heteromorphic ZZ/ZW sex chromosomes with accumulated telomeric-like repeats in the thick-tailed geckos further illustrate the exceptional diversity of sex-determining systems in geckos and add important information to our understanding of the evolution and phylogeny of sex-determining systems in reptiles.