Pseudomonas stutzeri is a saprophytic microorganism that rarely causes severe infections. In this report, a 28 days old male patient with meningomyelocele at birth was presented. The patient was admitted to the hospital with fever, and diagnosed as meningitis on the basis of physical examination and leukocytosis (blood: 16.380/mm3, cerebrospinal fluid (CSF): 130/mm3; 90% PMNL). Following diagnosis ceftriaxone therapy was started led to improvement in clinical and laboratory findings. However on the 20th day, the clinical signs and symptoms became worse, and the patient was diagnosed to develop a second meningitis attack by laboratory examination of CSF. P. stutzeri was isolated from the CSF culture, and the isolate was found to be resistant to ceftriaxone. Upon this result the therapy has changed to meropenem. On the 5th day of the therapy, the patient has slightly improved and he was discharged due to the wishes of his parents, however he died two days after discharge. This first case of P. stutzeri meningitis in neonates was presented to withdraw attention to this clinical entity.