Selective IgM deficiency (SIgMD) is a rare immunodeficiency disease with a reported prevalence of 0.03%. Most SIgMD in adult people is found in patients with malignant disorders or autoimmune diseases. We report a case of selective IgM deficiency associated with systemic lupus erythematosus (SLE). A 61-year-old female was admitted with severe cough and fever. There was no history of recurrent infection, and there was no family history of immunodeficiency or SLE. Computed tomography scan of the chest revealed interstitial infiltrates. Laboratory findings revealed pancytopenia, proteinuria and tests for anti-nuclear antibody and anti-DNA antibody were positive. Her serum IgM level was very low, lower than 7 mg/ml, while her IgA and IgG level were rather high. Renal biopsy showed ISN class V lupus nephritis, so she was diagnosed as SLE associated with SIgMD. She was treated with a pulse therapy of 500mg metylpredonisolone, followed by daily prednisolone (40 mg/day) and tacrolimus (2 mg/day), which was proved to be effective.