The recent focus on the bidirectional heart-brain interactions in psychoneurophysiological research has led to a variety of findings suggesting vagal activity is associated with cognition and, possibly, specifically with executive functioning. This systematic review and meta-analysis aimed to provide a better understanding of the association between vagally-mediated heart rate variability (HRV) and executive functioning. We included 13 correlational studies. We found a small positive association between vagally-mediated HRV and executive functioning (r = .19, 95% CI .15 to .23, p < .0001) using a quantitative synthesis of existing studies with random-effect models. Conducting meta-regression analyses, we found that vagally-mediated HRV predicts cognitive inhibition and cognitive flexibility more than working memory. In addition to the specific executive function measured, this relationship is moderated by the HRV measurement used, and age. After proposing a theoretical interpretation of the results, we emphasized the need for further research in light of the methodological issues identified in the included studies, and we outline several aspects to consider in future studies.