The aim of this study was to assess the prevalence of communication, and factors affecting communication between high school adolescents with their parents on reproductive health issues in Pokhara Metropolitan city, Nepal. A school-based cross-sectional study for quantitative and focus group discussion for qualitative study was done where data from adolescents were taken through self-administered questionnaire and information and data were collected from parents through focus group discussions. A multistage sampling technique was used to sample the study participants. Data were collected by using a self-administrated structured questionnaire, which was developed based on previous literature incorporating all variables to be assessed. Data were entered and analyzed through Epi data and SPSS version 20.0, respectively. This study revealed that 18.1% of students discussed RH issues with their parents. Factors such as being a male student (adjusted odds ratio [AOR] =3.36; 95% CI 1.57-7.17); being in the 11-12th grade (P value 0.001:95% CI 0.183-0.77), knowledge on RH issues (AOR =3.94; 95% CI 1.91-8.104); significantly affect the communication between parents and students on RH issues. This study showed that only a low proportion of students communicated on RH issues with their parents. Parents should focus on both male and female child equally, in discussing RH matters and in improving their communication skills, and should be transparent in the community to encourage open discussion among family members particularly with their adolescent children.