Most cases of guttural pouch mycosis present with epistaxis and/or neurologic deficits due to fungal damage to adjacent vessels and nerves. In this atypical case, the horse presented with unilateral nasal discharge, head tilt, and neck pain. Upon further diagnostics, the horse was found to have otitis media with resulting temporohyoid osteoarthropathy and atlanto-occipital joint infection. These are rare, but documented, sequela to guttural pouch mycosis. Treatment involved the ligation of affected vessels, systemic and topical antifungals, and ceratohyoidectomy to prevent temporohyoid fracture. The joint infection was treated with anti-inflammatories, analgesics, and appropriate antibiotic therapy. This paper will show the importance of diagnosing and treating complications of guttural pouch mycosis, as well as the importance of avoiding complications associated with surgical treatment.