The prevalence of hypertension has been decreasing in Japan due to improved medical treatment and a decrease in dietary salt intake. However, disparities in the prevalence, treatment, and control of hypertension are expected to occur in different regions. This study aimed to investigate the trends in the prevalence, treatment, and control of hypertension at the prefectural level of life expectancy among Japanese population. We used data from the National Health and Nutrition Survey and analysed the individual survey information of individuals aged 40–69 years by dividing it into six terms, i.e., 1995–1997, 1999–2001, 2003–2005, 2007–2009, 2012, and 2016. Prefectures were classified into four groups according to their 40-year-old life expectancy in 2000. Outcome values were standardised to the population by 10-year age groups in 2010, and they were tested by two-way analysis of variance according to six terms and life expectancies. The prevalence of hypertension tended to decrease, especially among women, whereas the treatment and control tended to improve from the first to the sixth period in both men and women. The prevalence and treatment of hypertension in men with longer life expectancy tended to be lower than that in other groups, and there was no obvious difference in the control. In women, there were no obvious differences in the prevalence, treatment, or control. Reducing the prevalence of hypertension by improving lifestyle factors, such as high salt intake in each prefecture with a relatively short life expectancy, may be important to resolve the disparity in life expectancy among prefectures.