Learning environments may shape both children's cognitive outcomes and the maturation of large‐scale neural dynamics. We investigate whether pedagogical context modulates brain activity and cognition in 96 students (4–15 years) enrolled in Montessori (MSC) or traditional (TSC) schools. Montessori emphasizes self‐directed exploration with increasing independence, whereas traditional classrooms shift from play‐based early learning to teacher‐directed instruction. To examine how neural development diverges across educational trajectories, we quantify the temporal asymmetry (“non‐reversibility”) of fMRI signals during resting state and movie‐watching. Behaviorally, MSC students outperform TSC peers in language, mathematics, and both divergent and convergent thinking. Neural patterns diverge with age: during rest, non‐reversibility increases in MSC but decreases in TSC, primarily in sensorimotor, dorsal attention, and frontoparietal networks; during movie‐watching, differences are strongest in younger children, especially in subcortical, visual, and default mode networks. Exploratory analyses reveal higher non‐reversibility in females, with larger sex differences in TSC. These findings suggest that pedagogical context may shape developmental trajectories and variability of neural dynamics. Montessori education may foster more adaptive brain dynamics, support flexible and creative thinking, and reduce gender disparities. Longitudinal research is needed to clarify what non‐reversibility reflects and how educational approaches sculpt brain development.