The current study aims to investigate the complication rate of equine appendicular magnetic resonance imaging (MRI) performed under general anesthesia at a tertiary referral center. 1655 horses, donkeys, and mules were included in the study. A complication rate of 1.5% was found in this 9-year study period. The most common complication was post-anesthetic fever with 11 horses becoming pyrexic in the immediate post-anesthetic period. Four of these horses went on to develop clinical pneumonia and one horse had an outbreak of respiratory herpesvirus. The incidence of neuropathy was 0.4% and colic was 0.4%. This study concludes that peri-anesthetic antimicrobial administration would not decrease the risk of complications in horses or donkeys undergoing general anesthesia for MRI of the appendicular skeleton at this tertiary referral center.