Gender differences in cooperative choices and their neural correlates were investigated in a situation where reputation represented a crucial issue. Males and females were involved in an economic exchange (trust game) where economic and reputational payoffs had to be balanced in order to increase personal welfare. At the behavioral level, females showed a stronger reaction to negative reputation judgments that led to higher cooperation than males, measured by back transfers in the game. The neuroanatomical counterpart of this gender difference was found within the reward network (engaged in producing expectations of positive results) and reputation-related brain networks, such as the self-control network (engaged in strategically resisting the temptation to defect) and the mentalizing network (engaged in thinking about how one is viewed by others), in which the dorsolateral prefrontal cortex (DLPFC) and the medial (M)PFC respectively play a crucial role. Furthermore, both DLPFC and MPFC activity correlated with the amount of back transfer, as well as with the personality dimensions assessed with the Big-Five Questionnaire (BFQ-2). Males, according to their greater DLPFC recruitment and their higher level of the BFQ-2 subscale of Dominance, were more focused on implementing a profit-maximizing strategy, pursuing this target irrespectively of others' judgments. On the contrary, females, according to their greater MPFC activity and their lower level of Dominance, were more focused on the reputation per se and not on the strategic component of reputation building. These findings shed light on the sexual dimorphism related to cooperative behavior and its neural correlates.