In this paper, we describe the historical transition of sexuality education in Japan and the direction of sexuality education taken by the Ministry of Education, Culture, Sports, Science and Technology (MEXT). Reproductive health/rights, a key concept in sex education, is also discussed. In Japanese society, discussion on sexuality has long been considered taboo. After the Second World War, sexuality education in Japan began as “purity education.” From 1960 until the early 1970s, physical aspects such as genital organs, function, secondary sexual characteristics, and gender differences were emphasized. Comprehensive education as a human being, including physiological, psychological, and social aspects, began to be adopted in the late 1970s. In 2002, it was criticized that teaching genital terms at primary schools and teaching about sexual intercourse and contraceptive methods at junior high schools were “overdue guidance” and “extreme contents.” Sexuality education in schools has become a problem and has stagnated for about 10 years. Currently, schools teach sexuality education that does not deviate from the MEXT course guidelines. The direction of MEXT regarding sexuality education should be examined from the basic position that sexual activity by children is inappropriate. Reproductive health/rights apply the concept of human rights to sexuality and reproduction. Reproductive health/rights are key concepts that support sex education and women’s health.