The benefits and proposed physiological mechanisms of eccentric exercise have previously been elucidated and eccentric exercise has been used for well over seventy years. Traditionally, eccentric exercise has been used as a regular component of strength training. However, in recent years, eccentric exercise has been used in rehabilitation to manage a host of conditions. Of note, there is evidence in the literature supporting eccentric exercise for the rehabilitation of tendinopathies, muscle strains, and in anterior cruciate ligament (ACL) rehabilitation. The purpose of this Clinical Commentary is to discuss the physiologic mechanism of eccentric exercise as well as to review the literature regarding the utilization of eccentric training during rehabilitation. A secondary purpose of this commentary is to provide the reader with a framework for the implementation of eccentric training during rehabilitation of tendinopathies, muscle strains, and after ACL reconstruction.