The purpose of this experiment was to determine if exercising horses, infected with influenza virus, exacerbates the severity of clinical disease. Eight horses were trained on a treadmill for 42 days and then challenged with aerosolised influenza A/equine/Kentucky/91 (H3N8). Following challenge, 4 horses (exercise group) continued training for 28 days, while the other 4 horses (nonexercise group) were confined to their stalls. All horses developed clinical signs within 36 h of challenge (fever, coughing, and mucopurulent nasal discharge) and clinical scores were greater in the exercise group. Horses developed fever from Days 1–11 post challenge (PC) and were tachypnoeic and tachycardic from Days 1–14 PC. All horses lost weight within 4 days PC, but the exercise group lost an average of 20 kg more than the nonexercise group. All horses developed pneumonia, and ultrasonography revealed pulmonary consolidation and oedema by Day 7 PC that was resolving by Day 14 PC. Endoscopy and transtracheal aspirates showed airway inflammation for up to 21 days PC. While the exercise group exhibited more severe signs of clinical disease, resolution occurred for both groups on approximately Day 14 PC, and no adverse effects were noted at the end of the study. However, the potential long term effects of exercising horses acutely infected with influenza virus are unknown. Until further research is conducted in this area, it appears prudent not to exercise affected horses.