The level of health in Japan is due to a number of factors including cultural habits, isolation, and a universal health care system. John Creighton Campbell, a professor at the University of Michigan and Tokyo University, told the New York Times in 2009 that Japanese people are the healthiest group on the planet. Japanese visit a doctor nearly 14 times a year, more than four times as often as Americans. Life expectancy in 2013 was 83.3 years - among the highest on the planet.

A new measure of expected human capital calculated for 195 countries from 1990 to 2016 and defined for each birth cohort as the expected years lived from age 20 to 64 years and adjusted for educational attainment, learning or education quality, and functional health status was published by the Lancet in September 2018. Japan had the highest level of expected human capital among the 20 largest countries: 24.1 health, education, and learning-adjusted expected years lived between age 20 and 64 years.

Obesity in Japan in 2014 was about 3.3%, about 10% of that in the United States, presumably because of the Japanese diet. It has the lowest rate of heart disease in the OECD, and the lowest level of dementia in the developed world.

Japan's suicide rate is high compared to the U.S. According to Mark D. West's systematic review Law in Everyday Japan: Sex, Sumo, Suicide, and Statutes, suicide rates have been at an elevated rate in Japan for 12 decades. In 1998, the suicide rate became more alarming as it increased, and it did not notably decrease until 2011. The Yomiuri Shimbun reported in June 2008 that more than 30,000 people had killed themselves every year for the past decade, and the suicide count remained over 30,000 for the 14th year running in 2011. A study published in 2006 suspects that health problems were a factor in almost 50 percent of Japan's suicides in 2006. However, the Yomiuri's 2007 figures show 274 school children were among those who took their own lives, in which bullying was often a contributing factor.

There are many factors to consider, but suicide rates overall appear to increase with age, as seen in the figure in this section. As of 2003, suicides of people in their twenties made up about ten percent, those in their thirties made up about twelve percent, those in their forties made up about sixteen percent, those in their fifties made up about twenty-five percent, and those in their sixties or older made up about thirty-three percent.

Although suicide is a priority health issue, Japanese culture views the act as something different than morally wrong and unacceptable. In fact, according to Young's 2002 article, traditional Japanese culture accepts suicide as a positive moral act characterizing the person's sense of moral duty to others which is driven by social context. Given that Japan is a collectivistic culture, moral duty to other members of society is important. Each individual is viewed as a part of the bigger group; everyone is considered a member of the group rather than as separated individuals. When a member feels that sacrificing their self would be best for the group as a whole, they are compelled to consider suicide as a viable option - they may believe that self-sacrifice is moral duty to the group. This is likely a part of the problem in trying to reduce the suicide rate. There is difficulty for psychiatrists and other mental health professionals in Japan to reduce the suicide rate when the act of suicide is, given the right circumstances, a completely rational and moral decision.^{[citation needed]}

One of the biggest public health issues is smoking in Japan, which according to Tadao Kakizoe (honorary president of the National Cancer Center) kills more than 100,000 people per year and is responsible for one in ten deaths.

A team led by Professor Osaki of Tottori University estimated the social cost of excessive drinking in Japan to be 4.15 trillion yen a year.