Background: Sexual and reproductive needs among adolescents remain largely unmet in Uganda, this coupled with poor access and utilization of adolescent sexual and reproductive health services among secondary school girls increases vulnerability to high risk sexual practices and adolescent pregnancy. This study aimed at evaluating the effect of providing school based sexual and reproductive health services on utilization of the services among school girls aged 15-19 years attending secondary schools in Uganda. Methods: The study used Cluster Randomized Controlled Trial (CRCT) design. Twenty secondary schools (clusters) were selected using cluster sampling and allocated 1:1 into control or intervention group stratified by geographical location. 1,182 (average cluster size of 60) girls aged 15-19 years were selected using simple random sampling. The intervention group received tailored Sexual and Reproductive Health (SRH) services information, in-school SRH services delivery and referral for a period of ten months. The control group received no intervention from the research team but had access to the usual public health care. Data was collected at baseline and end of study; descriptive statistics and inferential analysis was done as well as structural equation modeling using SPSS. Results: There was a significant variation in the proportion of school girls who reported receiving more than three services between the control group and intervention group (χ2 = 4.503, p = < 0.001). The findings indicate that the utilization of SRH services was higher (65.4%) among the girls who had access to School Based SRH services (intervention group) compared 34.6% among the girls who had access to services within the public/government health facilities (control group). Conclusion: Provision of School Based SRH services is an effective intervention for improving utilization of sexual and reproductive health services among school going adolescents. This is key in addressing the SRH needs of adolescents and promoting safe sexual practices.