Congenital dermal sinus is associated with meningitis caused by atypical pathogens. Although nosocomial infections with Enterobacter aerogenes in limited settings have been reported, community-acquired infections associated with congenital dermal sinus are rarely observed. We present the first non-neonatal case of a 3-month-old boy with meningitis due to Enterobacter aerogenes associated with congenital dermal sinus. The patient visited our hospital with fever and a skin dimple with lumbosacral hemangioma. He was diagnosed with meningitis based on cerebrospinal fluid (CSF) examination, which showed a cell count of 5717/µL. Subsequently, antimicrobial therapy with meropenem, cefotaxime (CTX), and vancomycin was initiated. His fever subsided, and the number of CSF cells decreased. Magnetic resonance imaging was performed for the dimple of the lumbosacral region, revealing the congenital dermal sinus. Enterobacter aerogenes was isolated from CSF and stool cultures, and treatment was adjusted to CTX alone based on susceptibility testing. However, the CSF culture remained positive. Although CTX was effective, the response to treatment was partial, and a switch to meropenem was required to achieve negative CSF cultures. In conclusion, Enterobacter aerogenes, although atypical, can cause community-acquired meningitis associated with congenital dermal sinus. Consistent with previous reports, in this case, a hemangioma on the back led to the diagnosis of congenital dermal sinus. Hence, systemic examination, including the back, is important. In addition, use of a third-generation cephalosporin (e.g., CTX) may not negate the CSF culture, even if it is effective. Thus, a switch to another drug (e.g., carbapenem) may be required.