Although enteroviruses generally cause asymptomatic or mild disease, neonates are at higher risk for severe illnesses, among which systemic disease characterized by multiorgan involvement is a potentially fatal condition. Enterovirus neonatal infections may be the source of nosocomial infections in neonatology or in pediatric intensive care units. We report central nervous system infections due to Echovirus 11 in two neonates and the molecular evidence of nosocomial transmission of this strain in a neonatal unit by enterovirus genotyping and phylogenetic analysis. This report illustrates the importance of including enterovirus genome detection in the sepsis screening concomitantly with bacteriological investigations performed at admission of a neonate. Rapid diagnosis and subsequent genotyping could have a beneficial impact on clinical practices at the individual level (reducing the length of antibiotic therapy) and public health policy at the collective level by reinforcing hygiene measures to prevent nosocomial infections, with nurseries and neonatal units being at greater risks.