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Within the context of learning, sometimes confusion is beneficial and other times it is detrimental. These seemingly disparate findings suggest that the benefits of confusion during learning may vary based on their dynamics, e.g., how confusion changes and corresponds to learning activities. In this study, we applied recurrence quantification analysis, a nonlinear computational approach, to examine the extent to which there were recurring instances of 79 undergraduates’ confused facial expressions during scientific-reasoning actions with a game-based learning environment, Crystal Island. Results suggested that learners achieved higher learning outcomes when they demonstrated more recurring instances of confused facial expressions during scientific-reasoning actions, but only when there was a restricted degree of agency during game-based learning.