Neisseria meningitidis is a major cause of bacterial meningitis worldwide, especially in children. Early diagnosis and empiric antibiotic treatment have led to a reduction in morbidity and mortality. The value of the traditional gold standard diagnostic tests, blood culture and cerebrospinal fluid (CSF) culture, has been adversely affected by preadmission use of parenteral penicillin and fewer lumbar punctures. We report a case of N. meningitidis in a 19-year-old male who was admitted after suffering from progressive severe headache, and intermittent high fever for 2 days. Gram stain and culture of CSF, and culture of throat swab were negative. However, N. meningitidis was detected by polymerase chain reaction (PCR) with a universal primer set and endonuclease digestion. This report indicated that the PCR method may be an alternative method for the rapid diagnosis of meningococcal meningitis.