The primary aims were to provide descriptive data on systemic and ocular complications associated with the treatment of equine keratomycosis. The secondary aims were to determine if complication rates differ between treatment types or are related to surgical and anesthetic factors. The study was a retrospective evaluation of 126 cases between 2004 and 2020 with confirmed fungal infection and recorded incidence of complications during hospitalization and surgical intervention if pursued. Additional information recorded included the size of the donor graft if utilized, time under general anesthesia, and prescribed medications. Fisher exact and χ2 tests were used to evaluate complication frequency differences. Logistic regression models determined the effects of donor graft size, anesthesia time, and duration of hospitalization on complication rates. Hypercreatininemia followed by colic were the most frequent systemic complications in the medical treatment group. Colic and conjunctival graft dehiscence were the most frequent systemic and ocular complications in all surgery treatment groups, respectively. The frequency of systemic complications did not vary between treatment groups, although colic rates were significantly higher following general anesthesia. All colic cases were resolved with supportive care. Donor graft size, anesthesia time, and duration of hospitalization did not impact complication frequency. The mainstays of medical therapy included topical fluoroquinolones, topical voriconazole, topical atropine, oral NSAIDS, and oral gastroprotectants. Treatment of keratomycosis is associated with a range of complications. Colic remains a significant risk, with increased frequency reported following general anesthesia. Reporting common complications associated with treatment aids in decision-making for equine clinicians and owners.