Introduction  The objective of this study was to identify measures Japan should take to achieve health (goal 3) and gender (goal 5) goals of the Sustainable Development Goals (SDGs) in synergy by comparing the status of health and gender in Japan and the United Kingdom based on gender analysis.Methods  In-depth interviews were conducted with 8 gender experts and 2 obstetrician/gynecologists in Japan and 9 informants in government, civil society and academia in the UK. The status of sexual and reproductive health and rights (SRHR) and measures against gender-based violence were elaborated. Qualitative content analysis was conducted on the transcripts of the interview audio-records.Results  We have compared contraception and abortion, control of sexually transmitted infections, sexuality education, measures against breast and cervical cancers and measures against gender-based violence in Japan and the UK. Significant differences were noted in contraception and abortion, sexuality education and measures against gender-based violence. There were four areas where the UK applied gender-transformative measures (measures that address not only the condition of women but also the gender relations between men and women and social status of women) whereas Japan has not yet applied such measures: 1) Ensuring selection of a wide range of contraceptive methods with low price, 2) Enabling abortion solely based on the decision by women, 3)Comprehensive sexuality education that includes gender and human relationship, and 4) Setting an integrated strategy against gender-based violence. Conclusion  Japan can strive for both health and gender goals of the SDGs by addressing above four aspects. Promotion of civil society participation in policy decision and increased proportion of female parliamentarians will help address these aspects.