Neonatal bacterial meningitis continues to be an important cause of mortality and morbidity worldwide. Escherichia coli possessing the K1 capsular polysaccharide is the most common Gram-negative pathogen causing neonatal meningitis. Here we present the complete genome sequence of neonatal meningitis-associated E. coli strain CE10, a unique K1 strain with a functional type III secretion system. Functional analysis of the genome should enhance our knowledge of the pathogenesis of neonatal E. coli K1 meningitis.