Repetitive motion is one risk factor associated with contraction-induced muscle injury, which leads to skeletal muscle degeneration, inflammation, and dysfunction. Since current methods are unable to quantify the acute degenerative and inflammatory responses of muscle tissue concurrently, the purpose of this study was to quantify the temporal myofiber response after exposure to injurious stretch-shortening cycles (SSCs) using a standardized stereological technique. Functional testing was performed on the ankle dorsiflexor muscles of Sprague-Dawley rats in vivo. Rats were anesthetized and exposed to 15 sets of 10 SSCs. Control rats were exposed to 15 sets of single isometric contractions of the same stimulation duration. Changes in muscle morphometry were assessed at 0.5, 24, 48, 72, and 240 h post-exposure to quantify the degree of myofiber degeneration and inflammation in the tibialis anterior muscle from each group. There was an increase in the volume density and average thickness of degenerating myofibers over time in the muscle collected from rats exposed to SSCs (p < 0.0001) that was significantly greater than in muscle exposed to isometric contractions at 24, 48, and 72 h post-exposure (p = 0.003). The volume density of degenerative myofibers was associated with functional deficits at 48 h. Stereological quantification of degenerative myofibers and interstitial space changes were associated with functional defects 48-72 h after SSC-induced injury, thus demonstrating stereology is an accurate measure of SSC-induced skeletal muscle injury.