BACKGROUND: Life expectancy in Japan has dramatically increased and is one of the highest in the world. However, the changes in lifespan in Japanese individuals with congenital diseases remain unknown. We investigated the secular changes in the lifespan of people with Down syndrome over the last 20 years. METHODS: We observed the secular trends in the number of stillbirths, deaths and the mortality rates at ages 20, 40, and 60 among all deaths registered with Down syndrome as the cause of death (ICD10 code: Q90) in the Japan national death registry database between 1995 and 2016. Changes in the median age at death between 1995-2005 and 2006-2016 were investigated based on sex and history of surgery. RESULTS: We identified 240 stillbirths and 1099 deaths in this period. The annual number of stillbirths and deaths above the age of 1 year increased, while the number of deaths below 1 year did not change. The proportional mortality indicator at ages 20, 40, and 60 increased from 21.7%, 11.7%, and 1.7% in 1995 to 69.9%, 66.7%, and 36.6% in 2016, respectively. The median age at death was higher in females, individuals without a surgical history, and deaths occurring in 2006-2016. The median age at death increased over the period in those without a surgical history. CONCLUSIONS: The age at death among people with Down syndrome has increased over the last 20 years, with currently 1 in 3 persons living over 60 years, necessitating adequate social welfare services in this aging population.