While the time course of muscle-tendon unit (MTU) function and structure following short (1 min) and long (5 min) durations of static stretching has already been investigated, less is known about medium stretch durations. Therefore, the purpose of this study was to investigate the time course of these parameters following 3 min of static stretching of the plantar flexor muscles. Fourteen healthy volunteers were tested on two separate days in a random order with two different rest times (0 min, 5 min) after 3 × 60 s of stretching. During each test, the dorsiflexion range of motion (RoM), passive resistive torque (PRT), and maximum voluntary contraction (MVC) were measured with a dynamometer. Ultrasonography of the gastrocnemius medialis (GM) muscle-tendon junction displacement and motion capture allowed us to determine the length changes in the tendon and muscle, respectively, and hence to calculate their stiffness. We observed an increase in RoM and a decrease in PRT and muscle-tendon stiffness at 0 min and 5 min post-stretching. This can be attributed to a decrease in muscle stiffness, as a decrease in PRT and muscle stiffness was observed up to 5 min after the stretching. No changes were detected in MVC torque and tendon stiffness. Static stretching for 3 × 60 s changes the muscle-tendon functions (RoM, PRT) for at least 5 min. These changes are related to mechano-morphological changes of the muscle, but not the tendon structure.