To investigate the morphological variation in an island population of the red fox (Vulpes vulpes), we measured 25 cranial and 24 dental characters for 225 specimens (137 males and 88 females) from Hokkaido Island, Japan. A Bayesian principal component analysis found only small differences among three groups identified genetically in previous studies. Concretely, analyses of variance and post-hoc tests detected clear differences in two functionally important measurements: postorbital constriction and upper fourth premolar length. In the postorbital constriction, relating to size of the temporal muscle, a difference with a gradient of increase from west to east on Hokkaido Island was found in both sexes. In the upper fourth premolar length, relating to body size, a difference between the Southern and Central groups was found in both sexes. Additionally, in differences in four measurements of skull width, skull height, mastoid width, and occipital condyle width, relating to braincase, were detected in only male. Subsequently, a correlation analysis showed that the postorbital constriction might be related to climatic conditions (e.g., minimum mean monthly temperature and snowfall). Endemic climate conditions and food habits appeared to contribute to the observed geographical variation in skull morphology.