Previous studies have demonstrated that paternal caregiving behaviors are reliant on neural pathways similar to those supporting maternal care. Interestingly, a greater variability exists in parental phenotypes in men than in women among individuals and mammalian species. However, less is known about when or how such variability emerges in men. We investigated the longitudinal changes in the neural, hormonal, and psychological bases of expression of paternal caregiving in humans throughout pregnancy and the first 4 months of the postnatal period. We measured oxytocin and testosterone, paternity-related psychological traits, and neural response to infant-interaction videos using fMRI in first-time fathers and childless men at three time points (early to mid-pregnancy, late pregnancy, and postnatal). We found that paternal-specific brain activity in prefrontal areas distinctly develops during middle-to-late pregnancy and is enhanced in the postnatal period. In addition, among fathers, the timing of the development of prefrontal brain activity was associated with specific parenting phenotypes.