Youth often face difficulties in accessing sexual and reproductive health services. The main aim this study was to determine the utilization of youth friendly reproductive health services among secondary school going youths of Fort portal Municipality and ascertain factors that influence use of these services. A cross sectional descriptive study was conducted on 250 secondary school youths in Fortportal Municipality. Sample size was determined by using Kish Leslie’s formula. Clustered sampling method was used to choose two (2) schools from each division of Fort portal Municipality; then respondents selected by consecutive sampling method. Data was analyzed using SPSS V.22. About half (53.2%) of the respondents were females and most of the study respondents (85.6%) were adolescents. Almost a third of the respondents (39.2%) were sexually active with 67.3 percent of them having unprotected sex. The study revealed that more than three quarters (79.2%) of the youths were poor users of youth friendly reproductive health services with sex education as the most utilized service (88.4%) and the least being use of contraceptives (20.3%). Age and availability of the services were the main determinants of utilization of these services. Adolescents utilized Youth friendly reproductive health services more than fellow older youths (P; 0.023 and P; 0.033 respectively). Availability of some Youth friendly reproductive health services in schools and health facilities influenced their utilization (P; 0.001 and P;0.013 respectively).Youth friendly reproductive health services are under-utilized by secondary school going youths. Youth friendly healthcare clinics should be operational in all schools and health facilities.