The early tetrapod Eoherpeton watsoni is known from the mid- to late Carboniferous (late Viséan to Namurian, approximately 346–313 Ma) of Scotland. The holotype is made up of a nearly complete but crushed skull with postcranial fragments. The skull anatomy of Eoherpeton was first described over 40 years ago; however, many details are obscured due to deformation of the specimen, including internal bone surfaces, the palatal bones and dentition, and suture morphology. Most phylogenetic analyses place Eoherpeton as an embolomere/reptilomorph on the lineage leading to amniotes, making it a key taxon for understanding anatomical changes during the fish-tetrapod transition. In this paper, we scanned the holotype using micro-computed tomography and digitally prepared the specimen. Based on these data, we present a revised description of the skull, including sutural morphology, that supplements and amends previous descriptions. New anatomical findings include the presence of a previously unknown tooth-bearing vomer, additional information on the shape of the basipterygoid processes and jaw joint, the ability to visualise the full extent of the pterygoid, and confirmation of the arrangement of the coronoid series. We also note the size of the pterygoid flange, which is larger than previously described for Eoherpeton. The pterygoid flange is widely considered to be characteristic of amniotes and serves as the origin of the medial pterygoideus muscle. The differentiation of the adductor muscles and appearance of medial pterygoideus are thought to have permitted a static pressure bite in amniotes, potentially resulting in greater bite forces and increased dietary range. Thus, the presence and extent of the pterygoid flange in Eoherpeton suggests this feature (and associated changes in feeding mechanism) may have evolved earlier than previously thought. Finally, the skull was digitally repaired and retrodeformed to create a new, hypothetical three-dimensional reconstruction of the skull of Eoherpeton.