Decision-making is one of the most crucial cognitive processes in daily life. An adaptable, rapid, and flexible decision requires integration between brain and body. Heart rate variability (HRV) indexes this brain–body connection and appears to be related to cognitive performance. However, its relationship with decision-making is poorly analyzed. This study investigates the relationship between HRV and the decision-making process, assessed through the Iowa Gambling Task (IGT). One hundred and thirty healthy university students (mean age = 23.35 ± 2.50) participated in the study. According to IGT performance, they were divided into high decision-makers (n = 79) and low decision-makers (n = 51). Heart rate variability was measured in the resting, reactivity (i.e., during IGT), and recovery phases. Higher vagally mediated HRV (vmHRV; indexed in frequency domain measures) was evidenced in good decision-makers in the resting, reactivity, and recovery phases. During the task, a higher vagal modulation after a first evaluation was highlighted in good decision-makers. In conclusion, HRV proves to be a valid index of inhibitory circuit functioning in the prefrontal cortex. The relationship with cognitive functions was also confirmed, considering the ability to inhibit disadvantageous responses and make better decisions.