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Abstract Background Behcet’s disease (BD) is a chronic immune-mediated, inflammatory disorder which may affect a number of different systems (oral and genital mucosa, eyes, skin, vascular district, joints, gastrointestinal tract and nervous system). Neurological manifestations are present in 5–10%, and gastrointestinal tract involvement in 10–15% of cases. The simultaneous involvement of two systems, neurological and gastrointestinal tract, is very rare and represents the aim of our case report. Case presentation We describe a case of a 12-year-old girl with neurological (endocranial hypertension, papilledema, retinal vasculitis) and gastrointestinal tract (terminal ileum and cecum inflammation) involvement and with a history of recurrent oral aphthosis; therefore, according to both International Criteria for Behcet’s Disease (ICBD) and Paediatric Behcet’s Disease criteria (PEDBD) the diagnosis of BD was confirmed. Conclusions This case report is one of the few described in literature with simultaneous involvement of the two systems, neurological and gastrointestinal tract, in paediatric BD. The diagnosis is really difficult because there is no specific diagnostic test. We think that our clinical case should help clinicians to suspect a BD with an unusual onset.