This study was designed to longitudinally analyze quantitative intramuscular and perimuscular fat and evaluate clinical outcomes according to healing degree after rotator cuff repair. From June 2013 through October 2018, patients who had undergone repair due to medium-sized rotator cuff tears and serial chest computed tomography (CT) preoperatively and at early (6-12 months) and late (at least 3 years) postoperative follow-ups were included. Supraspinatus (SST) intramuscular fat fraction ratio (IFFR) and perimuscular fat fraction ratio (PFFR) were calculated using chest CT. The rotator cuff integrity was categorized as healed, smaller retear (SRT), and larger retear (LRT) by comparing the preoperative tear size and retear size in shoulder CT arthrography at postoperative follow-ups. Clinical outcomes were evaluated using the American Shoulder and Elbow Surgeons (ASES) score, the University of California at Los Angeles (UCLA) shoulder rating scale, and the Constant score preoperatively and at early and late postoperative follow-ups. In the LRT group, compared with the preoperative values, there were increases in the SST IFFR and PFFR at the early (p = 0.002 and p = 0.006, respectively) and late (p < 0.001 and p < 0.001, respectively) postoperative time points. Late postoperative clinical scores (UCLA and Constant scores) were not improved compared to preoperative scores (p = 0.156 and p = 0.094, respectively). In the SRT group, there was no difference in the mean SST IFFR and PFFR between preoperative and early postoperative time points (p = 0.766 and p = 0.180, respectively), but the late postoperative values were higher than preoperative values (p = 0.009 and p = 0.049, respectively). Late postoperative clinical scores (ASES, UCLA, and Constant scores) in the SRT group improved compared to preoperative time (p < 0.001, p < 0.001, and p = 0.016, respectively). In the healed group, compared with the preoperative values, there was no difference in the mean SST IFFR and PFFR at postoperative time points; however, the late postoperative clinical scores (ASES, UCLA, and Constant scores) were improved (all p < 0.001). In the SRT group, IFFR and PFFR progressed in the late postoperative period and clinical scores improved over time. However, in the LRT group, IFFR and PFFR progressed in the early and late postoperative periods and clinical scores did not improve at the late postoperative follow-up.