This study investigated the effects of extracorporeal shockwave therapy (ESWT) on the subchondral bone and articular cartilage in the initiation of osteoarthritis of the knee in rats. Anterior cruciate ligament transected (ACLT) osteoarthritis (OA) rat knee model was used in this study. Twenty-seven male Sprague-Dawley rats were divided into three groups. The control group underwent sham surgery without ACLT and received no ESWT. The ACLT group underwent ACLT, but received no ESWT. The ACLT plus ESWT group underwent ACLT and received ESWT immediately after surgery. The evaluation parameters included radiograph, bone mineral density, serum levels of cartilage oligometric protein and osteocalcin, and urinary concentration of C-telopeptide of type II collagen (CTX-II), and histomorphological examination. At 12 weeks, OA of the knee was radiographically verified in the ACLT group, but very subtle changes were noticed in the control and the ACLT plus ESWT groups. On articular cartilage, the ACLT group showed significant increases in cartilage degradation and chondrocyte apoptosis compared to the control and ACLT plus ESWT groups. The ACLT plus ESWT group demonstrated significant decrease in the cartilage degradation and an increase in chondrocyte activity comparable to the control. In subchondral bone, the ACLT group showed a significant decrease in bone remodeling as compared to the control and ACLT plus ESWT groups. The ACLT plus ESWT group showed significant improvement in bone remodeling comparable to the control. Extracorporeal shockwave therapy shows chondroprotective effect associated with improvement in subchondral bone remodeling in the initiation of ACLT OA knee model in rats.