Muscle strain injuries are some of the most frequent injuries in sports, and command a great deal of attention in an effort to understand their etiology. These injuries may be the culmination of a series of subcellular events accumulated through repetitive lengthening (eccentric) contractions during exercise, and they may be influenced by a variety of variables including fiber strain magnitude, peak joint torque and starting muscle length. To assess the influence of these variables on muscle injury magnitude in-vivo, we measured fiber dynamics and joint torque production during repeated stretch-shortening cycles in the rabbit tibialis anterior muscle, at short and long muscle lengths, while varying the timing of activation prior to muscle stretch. We found that a muscle subjected to repeated stretch-shortening cycles of constant muscle-tendon unit (MTU) excursion exhibits significantly different joint torque and fiber strains when the timing of activation or starting muscle length are changed. In particular, measures of fiber strain and muscle injury were significantly increased by altering activation timing and increasing the starting length of the muscle. However, we observed differential effects on peak joint torque during the cyclic stretch-shortening exercise, as increasing the starting length of the muscle did not increase torque production. We conclude that altering activation timing and muscle length prior to stretch may influence muscle injury by significantly increasing fiber strain magnitude, and that fiber dynamics are a more important variable than MTU dynamics and torque production in influencing the magnitude of muscle injury.