Meningitis is a serious problem in newborn infants and has high mortality and frequent neurological sequelae. In neonates, signs and symptoms of serious infections are often obscure and clinical examination cannot distinguish septicemic babies with or without meningitis. Therefore, lumbar puncture is often not done in time and thus diagnosis of meningitis is missed. This study aimed to discover the prevalence of meningitis among these cases based on laboratory investigation. We prospectively enrolled the blood culture positive septicaemia cases which were not labeled as cases of meningitis during routine clinical evaluation. Out of 30 septicemic cases, eight (26.7%) had abnormal CSF cytology and biochemistry suggestive of meningitis. Among these eight cases, four had positive CSF culture; [Klebsiella pneumoniae (n = 3) and Pseudomonas aeruginosa (n = 1)], which were similar to the blood isolate of the respective patient. The clinical manifestations were similar in both septicemia and meningitis cases. Mortality was high among the meningitis cases compared with those having septicemia alone (37.5% vs. 13.3%), indicating the need for early diagnosis of this disease. Our data confirmed that it is important to do a lumbar puncture, along with blood culture, for all suspected septicemia cases.