Background In Ethiopia a number of efforts have been made to support sexual and reproductive health services (SRHS) for adolescents. However, there is limited information regarding the level of SRH utilization and associated factors among adolescents. Therefore, this study aimed to assess the magnitude of utilization of sexual and reproductive health services and associated factors among secondary school adolescents in youth friendly services (YFS) implemented and non-implemented areas of South Ari Woreda, South Omo zone, Southern Ethiopia, 2019. Methods Institution based comparative cross-sectional study with multistage stage sampling procedure was employed. Data were collected by self- administered questionnaire. The collected data were entered in to Epi Data version 4.4.1 software and then exported to SPSS version 20 statistical packages for further analysis. Descriptive statistics were computed and summarized by tables, frequencies, graphs, mean, and proportion. Both Bivariate and multivariable analysis were carried by using binary logistic regression. Variables with a p-value ≤ 0.25 in Bivariate logistic regressions were taken as potential candidate for multivariable logistic regression analysis to control confounders. Association between reproductive health services utilization and associated factors were reported by odds ratio at 95% CI. Variables having p-value less than 0.05 in multivariable logistic regression model were considered as statistically significant. Results The magnitude of SRHS in YFS implemented and non-implemented schools were 33.8% [95% CI (28.2-40.4)] and 9.4% [95% CI (5.6, 13.6)] respectively. Grade ten level adolescents and those who discuss SRH issues with their family members were three times [AOR=3.28, 95% CI (1.7, 6.29)] and [AOR=3.3, 95% CI (1.47, 7.41)] more likely to have sexual and reproductive health care-seeking behavior as compared to grade nine level adolescents and those who didn’t discuss respectively. Furthermore, adolescents who travel less than 30 minutes were six times [AOR=5.72, 95%CI, 2.58, 12.64] more likely to uptake the SRHS as compared to those travel more an hour. Conclusion The magnitude of utilization of SRH services were low in YFS non implemented school when compared to YFS implemented school. There is a need of more efforts to scale up SRHS in YFS non implemented schools among stakeholders at different hierarchies. In addition, it is better to promote open discussion with adolescents at family level, and emphasizes should be given for women education.