Childhood SLE (cSLE) has a higher prevalence of lupus nephritis (LN), and there are ethnic variations in response to treatment as well as outcome of LN. There are limited data on long-term outcome of LN in cSLE from the Indian subcontinent. Retrospective analysis of case records of patients with cSLE (satisfying revised American College of Rheumatology (ACR) 1997 criteria for diagnosis) and age of onset <18 years was conducted from 1989 to 2013. Data on clinical features, renal involvement and biopsy findings, treatment, renal outcome, damage accrual and mortality were collected. End-stage renal disease (ESRD) was defined as the need for renal replacement therapy. Actuarial ESRD-free survival was studied as the primary outcome measure using Kaplan-Meier analysis. Among 205 children with cSLE, 134 (121 girls) had evidence of LN. The mean age at disease onset was 13.7 ± 3.5 years and the mean disease duration at presentation was 1.9 ± 2.5 years. Kidney biopsy was available for 92 patients, and histology included: 13 (14.2%) Class II, 24 (26%) Class III, 43 (46.7%) Class IV and 12 (13.1%) Class V LN. The mean follow-up period was 6.75 ± 5.7 years. At last visit, 81 (60.4%) children were in complete remission, 28 (20.9%) were in partial remission, 15 (11.2%) still had active nephritis and 10 (7.4%) had progressed to ESRD. Almost two-thirds (62.9%) of patients experienced lupus flares, and mean flare rate was 0.09 flares/patient follow-up year. Fifty-six (43.8%) children accrued damage and the mean Systemic Lupus International Collaborating Clinics (SLICC)/ACR damage score was 0.79 ± 1.13. Actuarial ESRD-free survival at five, 10 and 15 years was 91.1%, 79% and 76.2%, and five-, 10- and 15-year renal survival was 93.8%, 87.1% and 84%, respectively. Although multiple factors individually predicted poor outcome (death/ESRD), only raised serum creatinine at onset (R square = 0.65, p ≤ 0.0001) and damage accrual (R square = 0.62, p ≤ 0.0001) remained significant on multivariate analysis. Eleven (8.2%) children died during the follow-up period, and infections were the leading cause of mortality. Long-term outcome of LN in cSLE in our cohort was better than previous reports from India. However, a high rate of major infection still remains the leading cause of mortality.