Lupus mesenteric vasculitis (LMV) as the first onset of systemic lupus erythematosus (SLE) in children is very rare. The clinical manifestations are abdominal pain, vomiting, diarrhea and other non-specific symptoms, which are easy to be misdiagnosed. A 13-year-old boy was admitted to Shanghai Children's Hospital who presented with abdominal pain and vomiting for 2 days. Physical examination on admission found that the child's abdominal muscles were tense and bowel sounds were weakened. Laboratory tests showed platelets of 30×10⁹/L, positive antinuclear antibody (1:320), positive anticardiolipin antibody IgM, decreased complement C3 and C4, weakly positive Coomb's test, and 24-hour urinary protein of 1.18 g. Abdominal CT showed significantly thickened and edema intestinal wall. After the patient was diagnosed with SLE and LMV, he was treated with 60 mg of methylprednisolone and hydroxychloroquine. The abdominal pain improved, but the platelet gradually decreased. After high-dose methylprednisolone and cyclosporine pulse therapy, platelet was still decreasing. After rituximab treatment, the patient's platelets gradually increased, and he was subsequently treated with belimumab. He was discharged after his condition stabilized. LMV can be the first manifestation of SLE. Abdominal CT has an important value in the diagnosis of LMV. Glucocorticoids can effectively alleviate the disease, but LMV is prone to relapse. Cyclophosphamide pulse therapy and rituximab may be effective in patients with relapse.