Horses and donkeys belong to the genus Equus, but important differences exist between the species, many of which affect their management and welfare. This study compared skull morphology between horses and donkeys. Horse (n = 14) and donkey (n = 16) heads were obtained post-mortem, sectioned sagittally close to the midline, and photographed for subsequent measurement of various skull structures. Skull, cranial, nasal, and profile indices were calculated for topographical comparisons between the species. The olfactory bulb area (OBA), OB pitch (the angle between the hard palate and the OB axis), and whorl location (WL) were also measured. A General Linear Model determined the main effect of species with Sidak’s multiple comparisons of species’ differences among the various measurements. There was no species difference in cranial or nasal indices (p > 0.13), but donkeys had a larger cranial profile than horses (p < 0.04). Donkeys had a smaller OBA (p < 0.05) and a steeper OB pitch (p < 0.02) than horses. The WL corresponded to the level of the OB in horses but was extremely rostral in donkeys (p < 0.0001). These results show clear differentiation in skull morphology between horses and donkeys. This may be useful in validating other physiological and behavioural differences between horses and donkeys.