This study assesses the cultural ecosystem service provision of 57,742 Shinto shrine forests in the 47 prefectures of Japan. Cultural values are an integral component of the ecosystem services framework and the development of non-monetary methods of valuing human health and cultural security is a research priority. Shinto shrine forests reinforce Japanese national identity, mores and community ties and have demonstrated physiological benefits for human health. A well-being index of the 47 prefectures of Japan, or “Happiness Ranking” is comprised of 40 objective indicators within the categories of 1) life and family issues, 2) labor issues, 3) safety and security issues and 4) medical care and health issues. Here we find that the number of Shinto shrine forests per 1000 people is positively correlated with the “Happiness Ranking” for the 47 prefectures. Shinto shrine forests provide cultural ecosystem services of cultural security and human health, increasing happiness across Japan.