We report a young woman with systemic lupus erythematosus (SLE) and an acute cerebellar ataxia. A history of poor appetite and vomiting preceded the inco-ordination. Ataxia in SLE has been well described, but is nevertheless uncommon. The clinical triad of mild confusion, ataxia and ophthalmoplegia also raised the possibility of Wernicke’s encephalopathy (WE). The diagnosis of WE was further supported by the magnetic resonance imaging features. Owing to overlapping causal factors, this case illustrates the complexity of diagnosing and managing neuropsychiatric syndromes in a patient with SLE. The limited published literature on SLE-related cerebellar syndromes adds to the challenge. Gastrointestinal manifestations of SLE are described as being common in SLE, with nausea and vomiting occurring in >50% of cases in some series. Poor eating habits and vomiting are well-described causes of non-alcoholic WE. This is the first description of gastrointestinal SLE as a possible cause of WE.