Tendinopathies are common injuries that typically occur from overuse and fatigue. Treatments target late-stage symptoms with limited success, leading to high rates of reinjury. Early intervention could halt tendinopathy progression to rupture but requires a better understanding of the biomechanical environment associated with early-stage disease. While fatigue injured tendons are further damaged by exercise that is initiated immediately after onset of injury, exercise that is initiated after a brief delay promotes repair. Similar macroscale mechanical properties and collagen damage throughout this delay period suggests that microscale, non-collagenous matrix changes after fatigue injury modulate tendon mechanotransduction and shifts the exercise response from detrimental to reparative. Glycosaminoglycans (GAGs) and proteoglycans (PGs) are increased during chronic tendinopathy, but their role in early-stage disease is unknown. We hypothesized that increased GAGs from fatigue injury modulate viscoelasticity and microscale strains to enable repair from exercise. Various GAG types were increased in the weeks after onset of fatigue injury in the extracellular and pericellular matrices of rat patellar tendons. Enzymatic removal of GAGs from these fatigued tendons increased microscale shear strain, suggesting that GAGs modulate the cell microenvironment after fatigue injury. GAG removal decreased dynamic modulus in the toe region and decreased loss tangent in the linear region of the stress–strain curve in fatigued tendons, suggesting the GAG increase modulates tendon multiscale mechanics and viscoelasticity during fiber uncrimping and fibril sliding and strain transfer. GAGs may influence repair in response to exercise and could serve as a therapeutic target for tendinopathy.