Mind–Body Physical Activity (MBPA) in educational settings is one possible preventive strategy for ameliorating stress-related physiological health parameters. The objectives of this study were to conduct a systematic review of the literature with meta-analyses on the effects of MBPA on stress-related physiological health markers in primary, secondary, and higher education students. In accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, the search for peer-reviewed articles published in English was conducted in PubMed, EBSCOhost, PsychInfo, Scopus, and Cochrane Library databases. Criteria for inclusion consisted of empirical studies targeting the student population (primary, secondary, higher education), studies examining the effectiveness of an MBPA intervention, studies including a control or comparison group (pre-test/post-test studies excluded), studies targeting physiological marker outcomes such as heart rate, blood glucose, cortisol, and blood pressure, and finally, studies examining interventions implemented within educational settings. Twenty-six interventions were eligible for the review and quantitative synthesis, which comprised a total of 1625 participants, with 783 students serving within the control/comparison group. There were statistically significant and large pooled effects for MBPA effectiveness for lowering heart rate (Hedges’ g = −1.71, 95% Confidence Interval (CI): −2.43, −0.98), cortisol (Hedges’ g = −1.32, 95% CI: −2.50, −0.16), and systolic and diastolic blood pressure (Hedges’ g = −1.04, 95% CI: −1.53, −0.58). These effects tended to be stronger in older students compared to younger students. Most analyses were characterized as having high heterogeneity and only 10 of the 26 studies were characterized as good quality (38.4%). MBPA interventions may have a positive impact on specific physiological health markers in students, especially in students within higher education. However, higher-quality research is needed in this area.