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Nonergodicity and Simpson’s paradox present significant, yet underappreciated challenges in neuroscience. Leveraging brain imaging and behavioral data from over 4,000 children and a Bayesian computational model of cognitive dynamics, we investigated brain-behavior relationships underlying cognitive control at both between-subjects and within-subjects levels. Strikingly, we observed a reversal of associations of inhibitory control brain activations with dynamic behavioral measures when comparing between-subjects and within-subjects analyses, revealing the nonergodic nature of these processes. This nonergodicity was pervasive throughout the brain but most pronounced in the salience network. Additionally, within-subjects analysis uncovered dissociated brain representations of reactive and proactive control processes, as well as distinct brain-behavior associations for individuals who adaptively versus maladaptively regulated cognitive control. Our findings offer insights into dynamic neural mechanisms of cognitive control during a critical developmental period. This work highlights the importance of embracing nonergodicity in human neuroscience, with implications for both theoretical understanding and applications to AI and psychopathology.