Systemic lupus erythematosus (SLE) is a systemic autoimmune inflammatory disease, which can affect almost all systems and organs. Gastrointestinal disorder is one of the most noteworthy complications of patients with SLE. However, gastrointestinal disorder with intestinal perforation is rare, but potentially life-threatening if not treated promptly. The present study reported a case of SLE with intestinal perforation, where surgical intervention was performed and a crevasse (~3 cm in diameter) was detected in the ileum, ~60 cm from the ileocecal valve. Following surgery, the patient suffered from difficult ventilator weaning, septic shock and intestinal obstruction. The patient was successfully treated and discharged from the hospital after ~4 months of treatment. Intestinal perforation in SLE patients is potentially life-threatening; early diagnosis and prompt treatment are crucial to the management of this rare complication of SLE.