Climate warming can influence sex determination and embryonic growth in oviparous reptiles that rely on external temperatures during development. Warmer incubation temperatures can stimulate growth in ectotherms until oxygen supply can no longer keep pace with growth rate; at which point metabolically expensive organs like the brain suffer. We aimed to understand the impact of heat and sex on brain development in central bearded dragons, Pogona vitticeps (Agamidae), a uniquely thermosensitive species that exhibits sex-reversal at warm incubation temperatures. Three sexual phenotypes are possible in P. vitticeps: genetically driven ZW females and ZZ males, with the latter phenotype thermally overridden at incubation temperatures >32 °C to induce ZZ sex-reversed females. To visualise changes in brain anatomy, we used buffered Lugol’s iodine to perform contrast-enhanced micro computed tomography (µCT) and synchrotron propagation-based phase-contrast CT scanning. A total of 57 embryos were sampled across developmental stages and incubated at two temperature treatments: cool (28 °C, n = 26) and warm (36 °C, n = 21). Using high-resolution models of neuroanatomy, we found that the telencephalic region of the forebrain is significantly larger in individuals with ZZ genotypes (males and sex-reversed females) compared to concordant ZW females. Although incubation temperature significantly influenced growth rate and body size during development, overall brain size was not significantly different across temperature treatments. Our results indicate that the effects of genotypic sex on brain development are more important than thermal influences, and thus the brain may be somewhat buffered to the effects of warm incubation temperatures in this arid-adapted dragon.