Introduction Concern regarding ability of autologous chondrocyte implantation (ACI) to correct for the bone and cartilage pathology of knee juvenile osteochondritis dissecans (JOCD) exists. The purpose of this study was to determine long-term, patient-based outcomes of ACI treatment of JOCD in young patients. Authors hypothesized long-term outcomes are comparable to reported mid-term outcomes. Methods A single institution, longitudinal cohort study design combining medical record review and outcome surveys was used. Inclusion criteria included isolated JOCD diagnosis, failed primary healing of operatively treated JOCD, ACI surgery > 5 years ago, and ≤20 years of age at time of ACI. Results 10/26 eligible patients (38.5%) participated (M: F = 5:5, age at ACI: 18.3 ± 2.5 y, current age: 30.8 ± 5.1 y, and current BMI: 24.6 ± 2.1). Follow-up was 12.0 ± 4.5 y. Lesion size at ACI was 9.1 ± 1.9 cm2. Femoral condyle location was medial = 6 and lateral = 4. All required treatment at some point for knee symptoms after ACI. During the past one year, four patients required treatment. Patient reported outcome scores at 12 years following ACI were IKDC score: 73.0 ± 3.6, KOOS scores including pain [88.7 ± 2.3], symptoms [78.2 ± 4.6], activity of daily living [94.7 ± 1.9], function, sports, and recreational activities [73.0 ± 5.3], and quality of life [57.5 ± 5.8], and Modified Cincinnati Knee Rating score was 77.9 ± 4.1. A moderate to good relationship was found between KOOS symptoms and BMI and lesion size. Function, sports, and recreational activities of the KOOS were greater in participants who had ≤1 lesion prior to ACI procedures (p = 0.044). Conclusion This study of ACI treatment of knee JOCD patients confirms sustained, long-term results. Number of lesions prior to ACI procedure influenced status of function, sports, and recreational activities.