The aim of this study was to quantitatively investigate the effects of extracorporeal shockwave therapy (ESWT) on the nanostructure and adhesion force of collagen fibrils in a rat model of collagenase-induced Achilles tendinitis (CIAT) using histology and atomic force microscopy. A total of 45 rats were divided into experimental groups of three rats each: a control group, 27 CIAT rats with nine time points, and 15 ESWT rats with five time points. Progressive changes in nanostructure including the fibrillary diameter and D-periodicity, and biomechanical properties including the fibrillary adhesion forces in each healing phase were investigated over a 5-week period after collagenase injection. On postoperative day 3, CIAT rats showed granulomatous tissue associated with subacute inflammation, and a deterioration in nanostructure and mechanical properties compared to controls. On postoperative day 12, the ESWT group showed increased vascularity, fibroblastic activity, lymphocyte and plasma cell infiltration, dense histocytes, and disorganization of the fibers compared to the CIAT group. The ESWT group showed and improvement in nanostructure and mechanical properties compared to controls, while the CIAT group showed a deterioration in nanostructure and mechanical properties compared to controls. On postoperative day 26, the ESWT group showed 30% inflamed tissue and 70% fibrotic tissue, while the CIAT group showed chronic inflammation. By the end of the experiments, in both groups the changes had reversed and the tissues were similar in appearance to those in the control group. Following ESWT the deformed and irregular collagen network returned to a well-aligned normal collagen network nanostructure. These results suggest that ESWT may promote the healing response in Achilles tendinitis.