In Japan, β-lactamase-nonproducing, ampicillin-resistant organisms have been evident among Haemophilus influenzae type b (Hib) isolates since 2000, when no appropriate vaccine had been approved. We therefore performed molecular analysis of agents causing H. influenzae meningitis nationwide over the following 10 years. Some 285 institutions have participated in surveillance since 2000. The capsular type and resistance genes of 1,353 isolates and 23 cerebrospinal fluid samples from pediatric patients with meningitis we had received from 2000 to 2011 were analyzed by polymerase chain reaction. Blood and spinal fluid test results obtained when patients were admitted were examined for correlation with outcomes. Hib was found in 98.9 % of isolates. We received more than 100 Hib isolates per year until vaccination began in December 2008, when these isolates decreased, especially since establishment of a special fund to promote vaccination in November 2010. Decreased incidence among infants 7 months to 2 years old has been particularly notable. However, the rate of ampicillin-resistant organisms has increased to more than 60 % of all isolates since 2009. We received 587 replies to a questionnaire concerning outcomes, indicating 2 % mortality and 17.7 % serious morbidity. Age of 6 months or younger and presence of disseminated intravascular coagulation at admission were related to an unfavorable outcome (p < 0.05), but ampicillin resistance was not. Combination therapy with third-generation cephem and carbapenem agents was used initially for 72 % of patients. Routine immunization can prevent Hib meningitis in children.