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Human behavior is surprisingly variable, even when facing the same problem under identical circumstances. A prominent example is risky decision making. Economic theories struggle to explain why humans are so inconsistent. Resting-state studies suggest that ongoing endogenous fluctuations in brain activity can influence low-level perceptual and motor processes, but it remains unknown whether endogenous fluctuations also influence high-level cognitive processes including decision making. Here, using real-time functional magnetic resonance imaging, we tested whether endogenous fluctuations in BOLD activity in the dopaminergic midbrain, encompassing substantia nigra and ventral tegmental area, influence risky decision making. We show that endogenous activity influences risk taking in humans with low pre-stimulus brain activity leading to more risky choice. Using computational modeling, we show that greater risk taking is explained by enhanced phasic responses to offers in a decision network. Our findings demonstrate that endogenous brain activity provides a physiological basis for variability in complex human behavior.