Introduction Evidence has shown that the experience of violence by a partner has important influences on women's risk of HIV acquisition. Using a randomized experiment in northeast South Africa, we found that a conditional cash transfer (CCT) targeted to poor girls in high school reduced the risk of physical intimate partner violence (IPV) in the past 12 months by 34%. The purpose of this analysis is to understand the pathways through which the CCT affects IPV. Methods HPTN 068 was a phase 3, randomized controlled trial in rural Mpumalanga province, South Africa. Eligible young women (aged 13-20) and their parents or guardians were randomly assigned (1:1) to either receive a monthly cash transfer conditional on monthly high school attendance or no cash transfer. Between 2011 and 2015, participants (N = 2,448) were interviewed at baseline, then at annual follow-up visits at 12, 24 and 36 months. The total effect of the CCT on IPV was estimated using a GEE log-binomial regression model. We then estimated controlled direct effects to examine mediation of direct effects through intermediate pathways. Mediators include sexual partnership measures, the sexual relationship power scale, and household consumption measures. Results We found evidence that the CCT works in part through delaying sexual debut or reducing the number of sexual partners. The intervention interacts with these mediators leading to larger reductions in IPV risk compared to the total effect of the CCT on any physical IPV [RR 0.66, CI(95%):0.59-0.74]. The largest reductions are seen when we estimate the controlled direct effect under no sexual debut [RR 0.57, CI(95%):0.48-0.65] or under no sexual partner in the last 12 months [RR 0.53, CI(95%):0.46-0.60]. Conclusions Results indicate that a CCT for high school girls has protective effects on their experience of IPV and that the effect is due in part to girls choosing not to engage in sexual partnerships, thereby reducing the opportunity for IPV. As a lower exposure to IPV and safer sexual behaviours also protect against HIV acquisition, this study adds to the growing body of evidence on how cash transfers may reduce young women's HIV risk.