Objective Febrile seizures may follow vaccination. Common variants in the sodium channel gene, SCN1A, are associated with febrile seizures, and rare pathogenic variants in SCN1A cause the severe developmental and epileptic encephalopathy Dravet syndrome. Following vaccination, febrile seizures may raise the specter of poor outcome and inappropriately implicate vaccination as the cause. We aimed to determine the prevalence of SCN1A variants in children having their first febrile seizure either proximal to vaccination or unrelated to vaccination compared to controls. Methods We performed SCN1A sequencing, blind to clinical category, in a prospective cohort of children presenting with their first febrile seizure as vaccine proximate (n = 69) or as non–vaccine proximate (n = 75), and children with no history of seizures (n = 90) recruited in Australian pediatric hospitals. Results We detected 2 pathogenic variants in vaccine‐proximate cases (p.R568X and p.W932R), both of whom developed Dravet syndrome, and 1 in a non–vaccine‐proximate case (p.V947L) who had febrile seizures plus from 9 months. All had generalized tonic–clonic seizures lasting >15 minutes. We also found enrichment of a reported risk allele, rs6432860‐T, in children with febrile seizures compared to controls (odds ratio = 1.91, 95% confidence interval = 1.31–2.81). Interpretation Pathogenic SCN1A variants may be identified in infants with vaccine‐proximate febrile seizures. As early diagnosis of Dravet syndrome is essential for optimal management and outcome, SCN1A sequencing in infants with prolonged febrile seizures, proximate to vaccination, should become routine. ANN NEUROL 2020;87:281–288