The Cognitive Science of Religion (CSR) is developing a sophisticated naturalistic account of religion, grounded in empirical research. However, there are limitations to establishing an empirical basis for theories about religion’s role in human evolution. Computer modeling and simulation offers a way to address this experimental constraint. A case study in this approach was conducted on a key theory within CSR that recently has come under serious challenge: the Supernatural Punishment Hypothesis, which posits religion facilitated the shift from small, homogeneous social units to large, complex societies. It has been proposed that incorporating empathy as a proximate mechanism for cooperation into the theory may address these challenges. To test this, we developed a computer simulation that runs iterated cooperation games. To assess the impact of empathy on cooperation, we developed an agent-based model with a baseline for empathetic concern, derived from neuroscientific literature on empathy and cooperation, that could be modulated by signals of religious identity. The results of this simulation may provide important data for an account of religion’s role in human evolution. Results and their implications, for both the theory and the modeling and simulation approach, are discussed.