We designed and validated a novel knee joint fixation/distraction system to study tendon–to-bone healing in an in vivo rat model of anterior cruciate ligament (ACL) reconstruction. The system uses an external fixator to apply a cyclic distraction of the knee joint while monitoring the resultant force developed across the joint, thus providing a temporal indication of structural changes during the healing process of the bone-tendon-bone reconstruction. The validation was performed using an optical kinematic tracking system to determine the local displacement of the knee. The average system compliance was determined to be with a coefficient of variation of 20.7%. The compliance was used to obtain a best fit correction factor which brought the total root mean square error of knee joint distraction to within (16.1%) of the applied distraction. We performed a pilot study using 15 rats that had ACL reconstructions using a flexor digitorum longus tendon autograft and found that the animals tolerated the indwelling fixator and daily anesthesia over a 10 day loading protocol. Our knee joint fixation/distraction system provides a valuable tool to study how mechanical stimuli affect in vivo bone-tendon-bone healing.