A five-year-old Oldenburg maiden mare presented for reproductive evaluation following several months, where the owner noticed the mare exhibiting irregular behavioral estrus. After an initial attempt to manage the mare with an estrus suppression medication, a more thorough investigation was performed, ultimately leading to the identification of several reproductive anatomical abnormalities and sex chromosome karyotyping, which allowed for the diagnosis of sex chromosome mosaicism. Based on a recent literature search, this is the first report of 64,XX/64,XY/63,XO mosaicism in a mare, where abnormal and irregular behavioral issues were the primary presenting sign. This report describes the clinical signs and diagnostic investigation that led to the eventual diagnosis and further discusses how such a common and seemingly innocuous presenting problem, can have a complex underlying etiology, with significant implications for the horse’s future working, and reproductive potential.