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Thrombotic microangiopathy (TMA) is generally diagnosed through clinical features characterized as microangiopathic hemolytic anemia, thrombocytopenia, and multiple organ injury, as well as by pathological findings such as vascular damage and endothelial cell injury. Rheumatic and autoimmune diseases could be accompanied by secondary TMA; in fact, systemic lupus erythematosus (SLE) is a common disease associated with secondary TMA, and SLE complicated with TMA has been reported to have a poor prognosis. Although TMA occurs rarely in pediatric SLE patients, it often leads to severe clinical conditions. Here, we report a rare case of severe juvenile-onset SLE complicated with TMA and kidney injury. The 5-year-old patient showed renal dysfunction, thrombocytopenia, hemolytic anemia, nephrotic syndrome, hypocomplementemia, and elevation of anti-dsDNA IgG levels. Kidney biopsy revealed mesangial proliferation and endocapillary proliferation, as well as plumped endothelial cells, with full-house pattern deposits in immunofluorescence study. Combination treatment of methylprednisolone pulse therapy followed by oral prednisolone, mycophenolate mofetil, and plasma exchange was effective, whereas eculizumab did not show therapeutic effects. The patient further showed recurrent deterioration, and we initiated intravenous cyclophosphamide in addition to combination treatment and eventually succeeded in controlling the disease. Genome analysis by whole-exome sequencing revealed no particular gene mutation related to either complement disorders or type-1 interferon. Further elucidations concerning the pathogenic mechanisms causing juvenile-onset SLE are needed to establish an efficient treatment strategy for TMA with SLE.