We describe a 12-year-old girl with systemic lupus erythematosus (SLE) who first presented with an atypical hemolytic uremic syndrome (HUS) associated with hypocomplementemia, and compare the clinical manifestations and prognosis between SLE patients with HUS and thrombotic thrombocytopenic purpura in the reported literature. Diagnoses were based on renal failure, hemolytic anemia, and thrombocytonemia, including the observation of fragmented red blood cells, hypocomplementemia and on the American College of Rheumatology criteria for SLE. Cocktail therapy may have been effective against the pathological condition of SLE. In 4 patients with SLE and HUS, prednisolone and immunosuppressive drugs were administered, and none of the patients suffered from chronic renal insufficiency. The prognosis for SLE patients with HUS is good. These findings suggest that SLE should be suspected in any HUS patient presenting with hemolytic anemia, thrombocytopenia, acute renal failure and hypocomplementemia, and the therapeutic response and prognosis for SLE with HUS are good.