We aimed to describe the clinical characteristics of West Nile patients reported in Québec in 2012 and 2013 and to document physical, mental and functional status 24 months after symptom onset according to illness severity. The cases were recruited by a public health professional. Data were collected from public health files, medical records and two standardised phone questionnaires: the Short Form-36 and the Instrumental Activities of Daily Living. In all, 92 persons participated in the study (25 had West Nile fever (WNF), 18 had meningitis and 49 had encephalitis). Encephalitis participants were older, had more underlying medical conditions, more neurological symptoms, worse hospital course and higher lethality than meningitis or WNF participants. Nearly half of the surviving hospitalised encephalitis patients required extra support upon discharge. At 24-month follow-up, encephalitis and meningitis patients had a lower score in two domains of the mental component: mental health and social functioning (P = 0.0025 and 0.0297, respectively) compared with the norms based on age- and sex-matched Canadians. Physical status was not affected by West Nile virus (WNV) infection. In addition, 5/36 (15%) of encephalitis, 1/17 (6%) of meningitis and 1/23 (5%) of WNF participants had new functional limitations 24 months after symptom onset. In summary, mental and functional sequelae in encephalitis patients are likely to represent a source of long-term morbidity. Preventive measures should target patients at higher risk of severe illness after WNV infection.