This study examined deaths due to unintentional injuries among children in Japan to identify the age groups and sexes at most risk, and the types of injuries, so that effective forms of targeted intervention can be devised. Among children aged 0–14 years, deaths whose underlying causes had been classified under code V01-X59 of the ICD-10 were defined as deaths of children caused by unintentional injuries. Using data from the Vital Statistics 2000–2009 for analysis, we examined the changes in mortality and trends in terms of sex, age, and cause of death. Mortality decreased by 46.2%, from 933 in 2000 to 502 in 2009. The mortality rate among children aged 1–4 years decreased by almost half. The total number of deaths during this decade was 7,362 (boys: 4,690, girls: 2,672). Among the causes of death, the majority were due to “transport accidents”, followed by “other accidental threats to breathing”, and “accidental drowning and submersion”. The characteristics observed in terms of sex, age, and cause of death—that is, deaths from suffocation among infants aged less than 1 year, drowning deaths among boys, and transport accidents involving pedestrians and cyclists—must be addressed as targets for future intervention.