This study aims to determine if baseline T1ρ and T2 will predict cartilage morphological lesion progression in the patellofemoral joint (PFJ) and patient-reported outcomes at 2-year after anterior cruciate ligament (ACL) reconstruction (ACLR). Thirty-nine ACL-injured patients were studied at baseline and two-year after ACLR. 3 T MR T1ρ and T2 images and Knee Injury and Osteoarthritis Outcome Score (KOOS) were acquired at both time points. Voxel-based relaxometry (VBR) technique was used to detect local cartilage abnormalities. Patients were divided into progression and non-progression groups based on changes of the whole-organ magnetic resonance imaging scoring (WORMS) grading of cartilage in PFJ from baseline to 2-year, and into lower (more pain) and higher (less pain) KOOS pain groups based on 2-year KOOS pain scores, separately. Voxel-based analyses of covariance were used to compare T1ρ and T2 values at baseline between the defined groups. Using VBR analysis, the progression group at 2-year showed higher T1ρ and T2 compared with the non-progression group at baseline, with the medial femoral condyle showing the largest areas with significant differences. At two-year, 56% of patients were able to recover with respect to KOOS pain. The lower KOOS pain group at 2-year showed significantly elevated T1ρ and T2 in the patella at baseline compared with the higher KOOS pain group. In conclusion, baseline T1ρ and T2 mapping, combined with VBR analysis, may help identify ACLR patients at high risk of developing progressive PFJ cartilage lesions and worse clinical symptoms 2-year after surgery.