Elizabethkingia anophelis is an emerging pathogen causing neonatal meningitis. Here, we describe the challenging course and necessity of a long 14-week duration of antibiotics in a 12-day-old male neonate with E. anophelis septicemia and meningitis. He developed ventriculitis and hydrocephalus, and needed a ventriculoperitoneal shunt. At 5-month follow-up he had developmental delay.