Childhood-onset systemic lupus erythematosus (cSLE) is a chronic inflammatory multisystem autoimmune disease that requires multiple differential diagnoses. Munchausen by proxy syndrome (MBPS) is a form of child abuse, where a caregiver intentionally creates a medical history and induces or fabricates signs or disease in a patient. To our knowledge, there is no case report of MBPS mimicking cSLE diagnosis. We reported herein a 9-year-old male patient, with a history of multiple hospitalizations due to seizures with altered levels of consciousness. The mother reported malar rash, photosensitivity, alopecia, arthralgia, arterial hypertension, macroscopic hematuria, seizure and positive antinuclear antibodies. In the other service, he was treated with intravenous methylprednisolone, prednisone and mycophenolate mofetil. At 8 years and 8 months, he was admitted to our tertiary center with history of fever and macroscopic hematuria. Laboratory examinations were normal, including negative for antinuclear antibodies, anti-double stranded DNA, anticardiolipin, anti-Ro/SSA, anti-La/SSB, anti-RNP and anti-Sm antibodies. Multiple urine cultures revealed the presence of Enterococcus faecium, Acinetobacter sp., Stenotrophomonas maltophilia and Serratia marcescens, without any association with pyuria. At 8 years and 9 months, he was readmitted at emergency room with history of severe fever, headache, vomiting, photophobia, phonophobia and dizziness. The physical examination showed agitation, confusion, ataxic gait, slurred speech, horizontal nystagmus, painful facial expressions, tachycardia and weight loss. Brain magnetic resonance angiography and cerebrospinal fluid analysis were normal. During hospitalization, he had an acute episode of epistaxis and otalgia with excoriation in the auditory canal. At that moment, the suspicion of MBPS mimicking cSLE was raised and phenytoin intoxication was confirmed (peak phenytoin concentration was 45.4 mcg/mL, therapeutic range 10–20 mcg/mL). The mother and the patient were immediately separated, and she was replaced by another legal guardian. One week later, the neurological and other signs and symptoms were completely resolved. The child was placed under paternal custody with a court order and moved to another state. After that, the mother reported phenytoin use for her child and was referred to psychiatric follow-up. In conclusion, the first case of MBPS mimicking cSLE, resulting in multiple unnecessary examinations and treatments with delayed diagnosis was reported.