Pulmonary aspergillosis in horses is a rare condition but can occur due to translocation of fungal elements through damaged intestinal mucosa secondary to enterocolitis. Disease progression is often insidious, with most cases of pulmonary aspergillosis diagnosed at post-mortem examination. This case study describes the development of pulmonary aspergillosis as a sequelae to Potomac Horse Fever in a fourteen year old Paint mare. The clinical presenation, dysbiosis due to prolonged antibiotic use, and translocation of microbes across damaged enteric mucosa, along with limited treatment options are discussed.