As scientists, we are keenly aware that if putative causes perfectly covary, the independent influence of neither can be discerned—a “no confounding” constraint on inference, fundamental to philosophical and statistical perspectives on causation. Intriguingly, a substantial behavioral literature suggests that naïve human reasoners, adults and children, are tacitly sensitive to causal confounding. Here, a combination of fMRI and computational cognitive modeling was used to investigate neural substrates mediating such sensitivity. While being scanned, participants observed and judged the influences of various putative causes with confounded or nonconfounded, deterministic or stochastic, influences. During judgments requiring generalization of causal knowledge from a feedback-based learning context to a transfer probe, activity in the dorsomedial pFC was better accounted for by a Bayesian causal model, sensitive to both confounding and stochasticity, than a purely error-driven algorithm, sensitive only to stochasticity. Implications for the detection and estimation of distinct forms of uncertainty, and for a neural mediation of domain-general constraints on causal induction, are discussed.