Magical ideation refers to beliefs about causality that lack empirical bases. Few studies have investigated the neural correlates of magical thinking and religious beliefs. Here, we investigate the association between magical ideation and religious experience in a sample of Vietnam veterans who sustained penetrating traumatic brain injury (pTBI) and matched healthy controls. Scores on the Magical Ideation Scale were positively correlated with scores on the Religious Experience Scale but only in pTBI patients. Lesion mapping analyses in subgroups of pTBI patients indicated that prefrontal cortex (PFC) lesions were associated with increased magical ideation scores, and this relationship was mediated by religious experience. Our findings clarify the mechanism by which the frontal lobe processes modulate magical beliefs. Suppression of the PFC opens people to religious experiences, which in turn increases magical ideation.