Background: sexual health in the military comprises a range of concerns including sexually transmitted infections (STI), unintended pregnancy, sexual violence and sexual dysfunction. This study aims to estimate the prevalence of sexual health concerns by gender in the French military and compare these prevalences to estimates in the general population. Methods: COSEMIL, the first sexual health survey in the French military comprises a probability sample of 1500 military personnel. Chi-square tests were used to compare lifetime abortion, STIs and sexual assault, and recent sexual dysfunction and sexual satisfaction by gender and explore the association between these indicators and current sexual risk (condom use at last intercourse). Results: women were more likely than men to declare negative sexual health outcomes, with the greatest difference related to sexual assault (24.3% versus 5.1% of males, p < 0.001) and sexual dysfunction hindering sexuality (15.2% of females versus 5.3% of males, p < 0.001). Women were also twice as likely to report ever having an STI (6.7% versus 3.4%, p = 0.03). Comparison with the French general population indicates lower percentages of STIs among military men (2.9% versus 4.9%) and higher percentages of abortion (17.6% versus 14.3%) forced sex (10.6% versus 7.4%) and sexual dysfunction (14.2% versus 9.3%) among military women. Conclusion: these results highlight gendered pattern of sexual health in the French military with women suffering greater sexual risks than men. Military health services should include women's health services to address the sexual and reproductive health gender gap.