Decision-making in social dilemmas is suggested to rely on three factors: the valuation of a choice option, the relative judgment of two or more choice alternatives, and individual factors affecting the ease at which judgments and decisions are made. Here, we test whether empathy—an individual’s relative ability to understand others’ thoughts, emotions, and intentions—acts as an individual factor that alleviates conflict resolution in social decision-making. We test this by using a framed, iterated prisoners’ dilemma (PD) game in two settings. In a behavioral experiment, we find that individual differences in empathic ability (the Empathy Quotient, EQ) were related to lower response times in the PD game, suggesting that empathy is related to faster social choices, independent of whether they choose to cooperate or defect. In a subsequent neuroimaging experiment, using functional magnetic resonance imaging, we find that EQ is positively related to individual differences in the engagement of brain structures implemented in mentalizing, including the precuneus, superior temporal sulcus, and dorsolateral prefrontal cortex. These results suggest that empathy is related to the individual difference in the engagement of mentalizing in social dilemmas and that this is related to the efficiency of decision-making in social dilemmas.