Few studies have investigated mediator effects of HIV prevention interventions on adolescents in sub-Saharan Africa. Herein, we report on a secondary analysis of an intervention that increased intentions to use condoms, abstain from sexual intercourse, and seek safe male circumcision among adolescents in Botswana. In a study conducted in Botswana, 806 grade 9 students from 21 public Junior Secondary Schools were randomly assigned to either the OWN THE FUTURE: Pulling Together We Will" ( PTWW) intervention group or a health promotion control group. Both conditions consisted of 12 1-h modules, with two modules delivered during each of the six sessions on six consecutive school days. The students in both groups completed confidential computer-based surveys at several time points: pre-, immediately post-, 3, 6, and 12 months post-intervention. Mediation was assessed using the product-of-coefficients approach in a generalized estimating equations (GEE) framework. The analyses showed that condom use beliefs were significant mediators of the intervention effect on the intention to consistently use condoms over time. Also, negative socio-cultural beliefs, prevention beliefs, and HIV/STI knowledge were significant mediators of the intervention's effects on the intention to abstain from sex. Additionally, normative beliefs, prevention beliefs, parental negotiation, and circumcision knowledge were significant mediators of the intervention's effect on intention to seek safe male circumcision. The mediation analysis delineated a theoretical model and isolated activities that positively impact condom use, abstinence from sex, and circumcision intentions of Batswana middle school adolescents.