The Arabian horse is predisposed to diseases affecting the head, including several surgical diseases, which could be attributable to skull morphology. Traditional surgical approaches to the paranasal sinuses of Arabians present several challenges. The objective of this study was to compare skull morphology of the Straight Egyptian Arabian (AR) to the Thoroughbred (TB), using Computed Tomography (CT). We hypothesized that the Arabian phenotype results in a different skull morphology than the TB, requiring special consideration for surgical planning. Measurements were taken from 29 clinically normal adult horses (15 AR and 14 TB). Standing skull CTs were performed. Fourteen gross and 9 CT measurements were taken. Several variables showed significant difference between groups, in all cases greater in TB than AR. Head length was significantly shorter in AR than TB. Ratios suggested that head length is relatively shorter relative to body height in AR. The length of the maxillary bone flap was significantly shorter in AR, consistent with the authors’ clinical experience of maxillary flaps being short and giving poor access to the maxillary sinus. This is likely due to their shorter facial crest. The AR group had a significantly smaller minimal height of the nasomaxillary aperture, predisposing them to poor sinus drainage. Limitations of this study included small sample sizes, as well as the AR group consisting only of the Straight Egyptian lineage. AR skull morphology differs significantly from TB making surgical approaches more challenging. Methods to improve sinus drainage should also employed when treating sinus disease in AR.