Introduction Systemic lupus erythematosus (SLE) is a multisystem disorder that may present with various symptoms. It may involve the gastrointestinal tract in a variety of ways; some of the most well-known ones are transaminitis, lupus mesenteric vasculitis, lupus enteritis and mesenteric vascular leakage. We describe a case of a patient with SLE who presented with a five-month history of diarrhea caused by eosinophilic enteritis. To the best of our knowledge, there are few cases reported in the literature of patients with SLE who initially present with chronic diarrhea due to eosinophilic enteritis. Case presentation A 38-year-old Persian Iranian woman was admitted with a five-month history of diarrhea and abdominal pain. A physical examination showed nothing abnormal. Initially, she had only lymphopenia and mild eosinophilia. No autoimmune or infectious etiology was detected to justify these abnormalities. A thorough evaluation was not helpful in finding the etiology, until she developed a scalp lesion similar to discoid lupus erythematosus. Computed tomography showed small bowel wall thickening. Briefly, she manifested full-blown SLE, and it was revealed that the diarrhea was caused by eosinophilic enteritis. Conclusion Considering SLE in a patient who presents with chronic diarrhea and lymphopenia may be helpful in earlier diagnosis and therapy. This is an original case report of interest to physicians who practice internal medicine, family medicine and gastroenterology.