Debate continues about the optimal treatment modality of lupus nephritis (LN). We compared the efficacy and safety of intravenous cyclophosphamide (CYC) and mycophenolate mofetil (MMF) for LN treatment in Korea. After searching for systemic lupus erythematosus (SLE) patients diagnosed between 1998 and 2007 with the diagnostic code of ICD10, we selected the 71 patients who were treated with CYC or MMF without any other immunosuppressant except systemic steroid. Composite outcome was defined as progression to end-stage renal disease (ESRD) and/or all-cause mortality. The initial manifestations of the CYC group were more severe than those of the MMF group. The mean daily MMF dose was 980 ± 100 mg for 21.67 ± 18.25 months. The mean monthly dose per CYC pulse therapy was 850 ± 30 mg for 17.04 ± 13.15 months. The incidence of composite outcome was 5/20 (25%) in the MMF group and 4/51 (7.8%) in the CYC group. The relative risk (RR) for composite outcome in the CYC group was 0.249 (95% CI for RR: 0.067–0.934, p = 0.039) compared with the MMF group with Cox’s hazard proportional analysis. In Kaplan–Meier analysis, the probability of composite outcome was lower in the CYC group than in the MMF group (Log rank test p-value = 0.026). The results of this retrospective study suggest that intravenous CYC therapy may be more efficacious in averting ESRD and death than MMF. These results need to be confirmed in a larger randomized controlled trial.