Tendon connects muscle and bone, facilitating movement of nearly the entire body. In the hand, flexor tendons enable flexion of the fingers and general hand function. Injuries to the flexor tendons are common, and satisfactory healing is impaired due to excess scar tissue and adhesions between the tendon and surrounding tissue. However, very little is known about the molecular and cellular components of flexor tendon repair. To that end, we have previously described a murine model of flexor tendon repair that recapitulates many aspects of healing in humans including impaired range of motion and decreased mechanical properties. Here we provide an in-depth description and demonstration of this surgical procedure to completely transect and repair the flexor digitorum longus (FDL) tendon in the hind paw of the mouse. This technique can be used to conduct lineage analysis of different cell types, assess the effects of gene gain or loss-of-function, and to test the efficacy of pharmacological interventions in the healing process. However, there are two primary limitations to this model: i) the FDL tendon in the mid-portion of the murine hind paw, where the transection and repair occur, is not surrounded by a synovial sheath. Therefore this model does not account for the potential contribution of the sheath the scar formation process. ii) To protect the integrity of the repair site, the tendon is release at the myotendinous junction, decreasing the mechanical forces of the tendon, likely contributing to increased scar formation. In addition, we demonstrate the use of the cytospin method to identify and quantify different cell populations during healing. Isolation of sufficient cells during the healing process for flow cytometric analysis has proved quite challenging; cytospin requires far fewer cells but allows for simple immunofluorescent labeling and quantification of cells or proteins of interest.