Tendinopathy is a common clinical condition that can often be attributed to overuse. Given the insidious, subclinical onset of overuse tendinopathy, relatively little is known about the disease process, including both damage induction as well as any reparative response. To better understand the disease process, we used fatigue as a model of overuse and developed a murine, in vivo, sub-rupture tendon fatigue model as well as an automated method for quantifying structural changes to the tendon that are a physical manifestation of fatigue damage accumulation. We used these techniques and others to investigate how tendon structure and function are altered during fatigue damage accumulation. We also contrasted the biological responses subsequent to fatigue of two mouse strains, C57BL/6J and MRL/MpJ, known to exhibit dramatically different reparative capabilities, and measured the effects of each biological response on the structure and function of fatigued tendons. We found that as fatigue damage is accumulated, tendon structure, measured via histology, changes progressively. Using our automated image analysis algorithm, we were able to reliably quantify those changes, allowing us to non-destructively measure the amount of fatigue damage instilled in the tendon. We also assessed function, measured via mechanical testing, and found that tendon function is altered subsequent to structural changes. Contrasting the effects of the biological responses between the two mouse strains, we found that C57BL/6J exhibited no change to structure or function through 8 weeks post-fatigue, while MRL/MpJ exhibited structural recovery by 4 weeks post-fatigue, and functional recovery by 8 weeks post-fatigue. Contrasting the biological responses themselves to identify a mechanism for MRL/MpJ's effective repair, we found that C57BL/6J exhibited decreased expression of inflammatory cytokines, while MRL/MpJ exhibited maintenance of naïve expression levels of inflammatory cytokines. This observation, in conjunction with the current notion in the literature, that MRL/MpJ's regenerative capability is a result of limited expression of inflammatory cytokines subsequent to acute injury, suggests that while high levels of inflammation lead to poor healing, some baseline level of inflammation is necessary for repair to take place. These findings provide insight into the effects of fatigue damage accumulation and repair, as well as those components of the biological response to fatigue that are necessary for effective repair.