We conducted a prospective multicenter, opened-label, parallel, randomized, controlled trial to compare tacrolimus (TAC) and mycophenolate mofetil (MMF) for induction and maintenance therapy in lupus nephritis (LN). Adult patients with biopsy-proven LN International Society of Nephrology/Renal Pathology Society classes III–V and active nephritis were to receive prednisolone (0.7–1.0 mg/kg/day for four weeks of run-in period and tapered) and randomly assigned to receive TAC (0.1 mg/kg/day) or MMF (1.5–2 g/day) as induction therapy for six months. All patients who had remission received azathioprine (AZA) 1–2 mg/kg/ day as standard treatment in the maintenance phase. The primary outcome was Systemic Lupus Erythematosus Disease Activity Index-2000 (SLEDAI-2K) at six and 12 months, and the secondary outcomes included renal SLEDAI, non-renal SLEDAI, modified SLEDAI-2K, immunity SLEDAI, and disease activity remission. Eighty-four patients were randomized. One patient who was randomized to the TAC group withdrew from the study immediately after randomization. Therefore, 42 patients received MMF and 41 patients received TAC. Disease activity remission rate and time to disease activity remission were similar in both groups. Twelve patients (28.57%) in the MMF group and 10 patients (24.39%) in the TAC group achieved disease activity remission. For disease activity scores, both regimens significantly improved SLEDAI-2K during induction and maintenance therapy. Overall, SLEDAI-2K score in the MMF group decreased more compared with the TAC group. In the MMF group, mean SLEDAI-2K decreased from 11.6 4.8 to 6.3 3.9 after induction therapy and to 5.4 4.4 after maintenance therapy. In the TAC group, mean SLEDAI-2K decreased from 9.0 3.7 to 6.3 5.1 after induction therapy and to 7.1 5.4 after maintenance therapy. Renal SLEDAI and modified SLEDAI-2K showed a similar pattern with SLEDAI-2K. In non-renal SLEDAI and immunity SLEDAI, both regimens also resulted in decreased disease activity scores during the first two months. After that the scores were slightly increased. In the MMF group, the scores were still lower than baseline but in the TAC group were not. In conclusion, disease activity remission rate was similar in the MMF and TAC groups. For disease activity score as measured by SLEDAI-2K, TAC was comparable with MMF during induction but MMF was more effective on disease activity of active LN classes III and IV at 12 months, especially in the renal system.