The Achilles tendon is a frequent site for degeneration, and advanced understanding of this pathology requires an animal model that replicates the human condition. The aim of this study was to explore whether intratendinous collagenase injection combined with treadmill running created a pathology in the rat Achilles tendon consistent with human Achilles tendinosis. Collagenase was injected into one Achilles tendon of 88 high-capacity running (HCR) rats, which were randomized into treadmill running and cage control groups. Running animals ran at speeds up to 30 m/min on a treadmill at a 15° incline for up to 1 h/d, 5 d/week for 4 or 10 weeks. Cage control animals maintained cage activity. Collagenase induced molecular, histopathological and mechanical changes within the Achilles tendon at 4 weeks. The mechanical changes persisted at 10 weeks; however, the histopathological and majority of the molecular changes were no longer present at 10 weeks. Treadmill running had minimal effect and did not exacerbate the collagenase-induced changes as there were no statistical interactions between the interventions. These data suggest combined intratendinous collagenase injection and treadmill running does not create pathology within the Achilles tendon of rats selectively bred for HCR that is consistent with human Achilles tendinosis.