Although researchers have developed prevention programs to reduce bullying, the results are mixed, and this may be due to a degree of uncertainty in their theoretical foundation. In particular, these programs share an emphasis on empathy as a personal attribute that can be enhanced among students through the application of specific curricula that will, in turn, contribute to a reduction in bullying behavior. However, the link between empathy and bullying is unclear, as is the ability of bullying prevention programs to actually impact student empathy. In this study, we used a cluster randomized trial (N = 15 middle schools, 1,890 students, 47.1% female, 75.2% White) to evaluate the impact of cooperative learning on bullying, and we evaluated whether these effects were mediated by empathy and peer relatedness. Our results indicated that cooperative learning can significantly reduce bullying, and that some of this effect is transmitted via enhancements to affective empathy. Cooperative learning also demonstrated significant positive effects on cognitive empathy, but this did not have an effect on bullying. We also found that the effects of cooperative learning on cognitive and affective empathy were mediated by improvements in peer relatedness. These findings add a degree of clarity to the literature, and also represent the first time, as far as we are aware, that an antibullying program has been found to have significant effects on both cognitive and affective empathy.