Heart rate variability (HRV) has been suggested as a biological correlate of self-control. Whereas many studies found a relationship between HRV at rest and self-control, effect sizes vary substantially across studies in magnitude and direction. This meta-analysis evaluated the association between HRV at rest and self-control in laboratory tasks, with a particular focus on the identification of moderating factors (task characteristics, methodological aspects of HRV assessment, demographics). Overall, 24 articles with 26 studies and 132 effects (n = 2317, mean age = 22.44, range 18.4–57.8) were integrated (random effects model with robust variance estimation). We found a positive average effect of r = 0.15, 95% CI [0.088; 0.221], p < 0.001 with a moderate heterogeneity (I2 = 56.10%), but observed evidence of publication bias. Meta-regressions did not reveal significant moderators. Due to the presence of potential publication bias, our results have to be interpreted cautiously.