Aerobic exercise could improve stretch-induced strength deficits. However, mechanisms of the improvement were unclear. The purpose of the study was to examine the effects of aerobic exercise after static stretching (SS) on flexibility and isometric strength in ankle plantar-flexor muscles. Fifteen healthy males received two interventions after SS of their ankle plantar-flexor muscles for 5 min. One was aerobic exercise for 10-min on a cycling ergometer, and the other was a 10-min rest as a control. Range of motion (ROM) of ankle dorsiflexion, passive torque at terminal ROM, muscle-tendon unit (MTU) stiffness, muscle tendon junction displacement, peak torque of ankle plantarflexion, and the amplitude of electromyography (EMG) were measured. Immediately after the SS, in both interventions, ROM, passive torque, and muscle tendon junction displacement increased significantly (p < 0.05), while MTU stiffness, peak torque, and the amplitude of EMG were significantly decreased (p < 0.05). After 10-min on a cycling ergometer, the decreased peak torque and amplitude of EMG indicated higher values than those before SS (p < 0.05), while MTU stiffness was no change. In conclusion, SS increased ROM because of the decreased MTU stiffness as well as increased tolerance for stretching. Aerobic exercise could increase the muscle strength and amplitude of EMG which decreased after static stretching.