The authors describe a one-year-old girl with a fronto-ethmoidal encephalomeningocele who developed wound infection, purulent meningitis and septic shock 5 hours after operation. The patient was treated with intravenous ceftazidime and vancomycin empirically. The cerebrospinal fluid (CSF) and eye discharge grew Streptococcus pneumoniae (S. pneumoniae). The minimal inhibitory concentration (MIC) by E-test of penicillin and cefotaxime were 1.0 and 0.38 ug/ml respectively so the antibiotics were switched to cefotaxime 300 mg/kg/day. She recovered completely after appropriate treatment. Penicillin-non-susceptible S. pneumoniae should be considered as one of the causes of post-operative serious infection of the face and neck in the era of increasing prevalence of penicillin-resistant S. pneumoniae.