The prevalence of adolescent pregnancy has remained high (25%) in Uganda for the last 10 years despite the implementation of numerous prevention programs. The limited access and availability of comprehensive reproductive health services by adolescents especially those in school increases vulnerability to risky sexual behaviour and consequently leading to pregnancy. This study aimed at evaluating the effectiveness of providing School Based Reproductive Health services on prevention of adolescent pregnancy in Uganda. Cluster Randomized Controlled Trial (CRCT) design was used and 1,182 school girls aged 15-19 years enrolled within 20 clusters. Results showed that provision of School Based SRH services (OR= 41.52; 95% CI 17.07-100.99; p < 0.001) had a statistically significant effect on the occurrence of adolescent pregnancy among school girls aged 15- 19 years attending secondary school. Therefore provision of School Based reproductive health services is an effective intervention in the prevention of adolescent pregnancy among school girls.