Objectives: To evaluate the effect of functional movement screen (FMS)-based functional exercise in patients after anterior cruciate ligament reconstruction (ACLR). Design: Randomized, controlled, single-blind trial. Setting: Institutional, single center. Patients: A total of 38 patients who underwent ACLR were recruited and randomly assigned to group 1 (n = 19) or group 2 (n = 19). Interventions: Both groups received 6-month routine rehabilitation immediately after surgery. From the postoperative fourth to sixth month, group 1 received FMS-based functional exercise plus routine rehabilitation and group 2 received routine rehabilitation only. The FMS-based functional exercise was individualized and customized functional corrective exercise, which was designed based on the 3-month postoperative FMS results. The frequency of rehabilitation was 1 hour per session, twice a week, for a total duration of 6 months. Main Outcome Measures: At 3 and 6 months postoperatively, patients were evaluated by FMS scoring, Lysholm Knee Score, and International Knee Documentation Committee 2000 Score. Results: After the intervention, both groups had significantly increased FMS, Lysholm Knee Score, and International Knee Documentation Committee 2000 score. Group 1 had significantly greater changes in FMS (median: 4 vs 3, P < .001), Lysholm Knee Score (median: 24 vs 16, P = .001), and International Knee Documentation Committee 2000 Score (median: 22 vs 8, P < .001) than group 2. Conclusion: The application of FMS-based functional exercise to patients after ACLR resulted in significant improvement in knee function and movements. The authors suggested integrating FMS evaluation and FMS-based training into routine post-ACLR rehabilitation programs.