Investigations of kinetic asymmetries during bilateral squats following anterior cruciate ligament reconstruction (ACLR) are limited to mainly cross-sectional studies and discrete value data extracted at specific knee angles. We assessed loading asymmetries during squats longitudinally throughout rehabilitation using curve analysis and compared patient-reported outcome measures (PROMs) between those with and without asymmetry. Bodyweight squats were performed by 24 individuals (13 females) post-ACLR on three occasions: (1) Early 2.9 (1.1) months; (2) Mid 8.8 (3.1) months; (3) at Return to Sport (RTS) 13.1 (3.6) months; and 29 asymptomatic controls (22 females) once. Time-normalized between-leg asymmetry curves of sagittal plane hip, knee, and ankle moments and vertical ground reaction forces were compared using functional data analysis methods. Individual asymmetrical loading for ACLR was classified when exceeding the 95% confidence interval of controls during ≥50% of the squat. At Early, ACLR had greater asymmetry than controls for knee (15%–100% eccentric phase; 0%–100% concentric) and ankle flexion moments (56%–65% concentric). At Mid, ACLR had greater asymmetry for knee (41%–72% eccentric) and ankle flexion moments (56%–69% concentric). No between-group differences were found at RTS. From Early to RTS, ACLR reduced asymmetry for hip (21%–46% eccentric), knee (27%–58% concentric), and ankle flexion moments (21%–57% eccentric). At Early, 11/24 underloaded their ACLR knee and 1 overloaded compared with controls. At RTS, 4 underloaded and 6 overloaded. No differences in PROMs were found based on loading asymmetry. Beyond the early phase of rehabilitation from ACLR, individual-level analyses are required to reveal differing loading strategies during bilateral squats.