We previously demonstrated with functional magnetic resonance imaging (fMRI) that religious belief depends upon three cognitive dimensions, which can be mapped to specific brain regions. In the present study, we considered these co-activated regions as nodes of three networks each one corresponding to a particular dimension, corresponding to each dimension and examined the causal flow within and between these networks to address two important hypotheses that remained untested in our previous work. First, we hypothesized that regions involved in theory of mind (ToM) are located upstream the causal flow and drive non-ToM regions, in line with theories attributing religion to the evolution of ToM. Second, we hypothesized that differences in directional connectivity are associated with differences in religiosity. To test these hypotheses, we performed a multivariate Granger causality-based directional connectivity analysis of fMRI data to demonstrate the causal flow within religious belief-related networks. Our results supported both hypotheses. Religious subjects preferentially activated a pathway from inferolateral to dorsomedial frontal cortex to monitor the intent and involvement of supernatural agents (SAs; intent-related ToM). Perception of SAs engaged pathways involved in fear regulation and affective ToM. Religious beliefs are founded both on propositional statements for doctrine, but also on episodic memory and imagery. Beliefs based on doctrine engaged a pathway from Broca's to Wernicke's language areas. Beliefs related to everyday life experiences engaged pathways involved in imagery. Beliefs implying less involved SAs and evoking imagery activated a pathway from right lateral temporal to occipital regions. This pathway was more active in non-religious compared to religious subjects, suggesting greater difficulty and procedural demands for imagining and processing the intent of SAs. Insights gained by Granger connectivity analysis inform us about the causal binding of individual regions activated during religious belief processing.