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Objective We aimed to compare the incidence of severe infections between mycophenolate mofetil (MMF) and other immunosuppressants in patients with systemic lupus erythematosus (SLE) on maintenance therapy using data from the Lupus Registry of Nationwide Institutions in Japan.Methods This study employed a prospective cohort design, including patients with SLE undergoing maintenance therapy. Exposure was defined as MMF treatment, and the control group included individuals who received other immunosuppressants (non-MMF) treatments. Severe infections requiring hospitalisation were the primary outcomes, whereas secondary outcomes included all-cause hospitalisation, changes in prednisolone dosage, disease activity and organ damage. Statistical analyses employed marginal structural models with stabilised inverse probability of treatment weighting to adjust for confounders.Results The analysis included 1004 patients; the incidence of severe infections was 6.5% in the MMF group and 7.5% in the non-MMF group, with no significant difference (OR 0.69, 95% CI 0.34 to 1.39). Similarly, all-cause hospitalisation rates were comparable between the groups (OR 0.72, 95% CI 0.47 to 1.09). Prednisolone dosage was significantly reduced in the MMF group (−0.66 mg/day, 95% CI −1.09 to −0.23). The organ damage score was modestly reduced in the MMF group (−0.19 points, 95% CI −0.37 to −0.01), whereas the change of disease activity score was comparable between the groups (−0.10 points, 95% CI −0.74 to 0.55).Conclusions MMF does not significantly increase the risk of severe infections compared with other immunosuppressants in SLE maintenance therapy. MMF may contribute to reducing the dose of prednisolone.