Systemic lupus erythematosus (SLE) is an autoimmune disease with multiple manifestations in several organs and systems. Neuropsychiatric manifestations can occur in 22-95% of paediatric cases, being much less frequent as an initial clinical event. We report a case of SLE, presenting primarily with neuropsychiatric symptoms. An African-descendant 7-year-old girl was admitted with a 4-day history of ataxia, diplopia and morning vomiting, as well as severe headache, psychiatric symptoms and cognitive dysfunction beginning 1 year prior to admission. Brain MRI was suggestive of encephalitis. Investigation excluded infectious aetiology. Immunological markers revealed high titre of antinuclear and anti-double-stranded DNA antibodies. Neuropsychiatric lupus (NPL) was considered, and cyclophosphamide and methylprednisolone pulses were started, with good initial response. Clinical deterioration motivated therapy with azathioprine with subsequent clinical stabilisation and a latent cognitive dysfunction. In unusual encephalitis presentation, a wide range of differential diagnosis has to be considered. Primary NPL presents difficult diagnostic and therapeutic challenges.