Aim  Little is known about basilar artery stroke (BAS) in children. The objective of this study was to calculate the incidence of BAS in children and to analyse the clinical presentation, risk factors, radiological findings, therapeutic approaches, and outcome of BAS in childhood.Method  A prospective, population‐based study including children with arterial ischaemic stroke and a systematic review of the literature was undertaken.Results  Seven children with BAS were registered at the Swiss Neuropaediatric Stroke Registry between January 2000 and June 2011 (incidence 0.037 per 100 000 children per year, 95% confidence interval [CI] 0.013–0.080). A further 90 cases were identified through the literature search. The majority of patients were male (73 males, 24 females) and the median age was 9 years (interquartile range [IQR]=6–13y). The median Pediatric National Institutes of Health Stroke Scale (PedNIHSS) score was 15 (IQR=4–27). Presenting signs and symptoms comprised impaired consciousness (n=64), quadri‐ or hemiparesis (n=58), bulbar dysfunction (n=46), vomiting, nausea (n=43), and headache (n=41). Prodromes occurred in 43% of cases. Aetiology was largely vasculopathic (n=38), but often unknown (n=40). Time to diagnosis varied from hours days; six patients received antithrombotic, thrombolytic, or mechanical endovascular treatment 12 hours or less after symptom onset. Outcome was good (modified Rankin Scale 0–2) in 45 patients; eight died. PedNIHSS score of up to 17 was a prognostic factor for good outcome.Interpretation  BAS is rare in children. Compared with adults, outcome is more favourable despite a considerable delay in diagnosis and treatment. Outcome was better in children with a PedNIHSS score of 17 or less.