Cooperation is essential for the functioning of human societies. To better understand how cooperation both succeeds and fails, recent research in cognitive neuroscience has begun to explore novel paradigms to examine how cooperative mechanisms may be encoded in the brain. By combining functional neuroimaging techniques with simple but realistic tasks adapted from experimental economics, this approach allows for the discrimination and modeling of processes that are important in cooperative behavior. Here, we review evidence demonstrating that many of the processes underlying cooperation overlap with rather fundamental brain mechanisms, such as, for example, those involved in reward, punishment and learning. In addition, we review how social expectations induced by an interactive context and the experience of social emotions may influence cooperation and its associated underlying neural circuitry, and we describe factors that appear important for generating cooperation, such as the provision of incentives. These findings illustrate how cognitive neuroscience can contribute to the development of more accurate, brain-based, models of cooperative decision making.