This paper aims to provide insight into the etiology and differential diagnosis of a rare severe pathological lesion in an isolated equine tooth from the medieval site of Crkveno Brdo. The site is located in the southern part of the Carpathian Basin, that is, in the northern part of present‐day Serbia near Senta, some 9 km south‐west of the town center in the vicinity of the village of Gornji Breg. The specimen presented in this study comes from the cultural layer dated to the period between the 14th and the 15th centuries. A healed oblique fracture was present in the right upper second premolar (106) of a horse (Equus caballus) 7–10 years of age. The specimen was subjected to an interdisciplinary approach, including identification of species and tooth type, and assessment of age at death, employing microcomputed tomography (microCT), and histopathology to differentially diagnose the pathological condition. The obtained results were additionally compared with findings in an apparently similar modern case of known etiology.