The Early Carboniferous stem tetrapod Whatcheeria deltae is among the earliest-branching limbed tetrapods represented by multiple near-complete specimens, making it an important taxon in understanding the vertebrate water-to-land transition. However, all preserved skulls of Whatcheeria suffer from post-mortem crushing and lateral compression, which has made cranial reconstruction problematic. In this study, computed tomography data of three Whatcheeria specimens were segmented using visualization software to digitally separate each individual skull bone from matrix. Digital methods were used to repair and retrodeform the bones and produce the first complete three-dimensional skull reconstruction of Whatcheeria. We provide a revised description of the cranial and lower jaw anatomy of Whatcheeria based on CT data, focusing on sutural morphology and previously unknown anatomical details. Our findings suggest that Whatcheeria had one of the narrowest skulls of any known early tetrapod, a gap between the nasals, and significant overlap of the lacrimal onto the nasal and prefrontal. Sutural morphology is used to infer loading regime in the skull during feeding and suggests the skull of Whatcheeria was well adapted to resist stresses induced by biting large prey with its enlarged anterior fangs.