Background: Nepal has a relatively young and growing population, like most low-income countries. Recently, Nepal has accelerated its commitment to the International Conference on Population and Development (ICPD) Programme of Action by introducing a programme focusing on the sexual and reproductive health of adolescents. This paper aims to report the sexual health knowledge, attitudes and behaviour of adolescents in rural Nepal. Methods: A survey was conducted in four districts of Nepal with representative sample among adolescents aged 15–19 years using pre-tested structured questionnaire in 2011. Questionnaire contents socio-demographic questions including knowledge, attitudes and behaviours related to reproductive and sexual health. The study was approved by the Nepal Health Research Council. Results: A total 3041 adolescents (mean age 16.4 years, 49.4% male and 50.6% female) completed the questionnaire. The data indicated that HIV/AIDS and other reproductive and sexual health knowledge among the respondents was moderate. Male respondents have better knowledge on HIV/AIDS compare to female respondents. Similarly, male have better access to modern means of communications. Both male and female were equally likely to say that they had used a condom the last time they had sex. A small proportion of all respondents (9.3%) had acquired emergency contraception, two thirds of those were male (65%) and among total users of emergency contraceptives, 85% were unmarried. Conclusions: Both education and youth-friendly services, targeting to female adolescents are required to improve the sexual health status of adolescents. The findings have important implications for the (re-)development sexual health interventions for adolescents in Nepal.