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Background: Self-regulation promotes engagement within the classroom. At a physiological level, a good indicator of the ability of the system to self-regulate is cardiac vagal tone (CVT). Aims: The present study aims to assess children's change over time (1 year) in their parasympathetic regulation (by way of CVT) in response to a social and cognitive stressor. Moreover, it addresses whether, if present, this change over time in regulation influences students' engagement in classroom activities while also accounting for classroom climate. Sample Forty-nine second graders were assessed at two time points: November 2018 (T1) and 1 year later in 2019 (T2). Methods: Children's CVT was registered at rest and while performing a stressful task during which they were asked to cognitively perform while being socially evaluated. Children were also interviewed on how much they feel engaged in classroom activities and their perceptions of classroom climate. Results: A repeated measures analysis of variance including 2 Time Points ×2 Phases of CVT Registration (baseline and during the stressful task) revealed a significant decrease in cardiac vagal activity from baseline to the task at T1, indicating that initially most children were not able to self-regulate and gave way to a stress response when facing the stressful task. The pattern changed at T2 when an active regulation took place signalled by an increase in CVT from baseline to the stressful task. Data analysis also revealed that among children who perceived a poorer classroom climate, the display of greater parasympathetic regulation over time was linked with higher active engagement in classroom activities. Conclusions: Growth in physiological regulation in response to a challenging task is associated with better engagement in classroom activities. Interventions and educational practice promoting the development of self-regulation strategies are recommended.