In developed countries, the infection related-mortality rates in children hospitalized in tertiary medical facilities, where many patients with underlying disease are also hospitalized, are uncertain. We investigated the characteristics of infectious diseases-related fatal cases in the pediatric ward of a Japanese tertiary medical facility. A total of 188 patients who died in the pediatric ward or intensive care unit at Kyushu University Hospital from 2002 to 2011 were enrolled. The patient characteristics were investigated based on their medical records. A total of 35 patients died of infections, 31 of whom had underlying diseases. Most patients died of sepsis or pneumonia (n = 27). All 9 patients who died within 7 days of birth were premature. Nine of the 13 patients with malignancy or hematological disorders died of hematopoietic stem cell transplantation (HSCT)-associated infections. The ratio of infectious disease-related fatal cases to the total cases decreased in the latter half of the study period. In particular, the proportion of preterm infants who died of infections was significantly lower in the latter 5 years (p = 0.02). Many of the infectious disease-related fatal cases were in premature infants and HSCT or post-HSCT patients. However, the mortality due to infectious diseases decreased in these patient groups.