•Two different antisaccade tasks were applied to investigate cognition, affect, and HRV.•We induced sadness and emotional arousal compared to a neutral control group.•Higher HRV reactivity predicted inhibitory control performance in the sadness group only.•Lower error rates were related to higher HRV reactivity.•Negative affect moderated the effect of HRV reactivity on inhibition of emotional stimuli. Higher negative affectivity has an association with decreased executive function and cognitive control. Heart rate variability (HRV) serves as an index of cardiac vagal regulation differences in the autonomic nervous system for both cognition and emotion. The current study investigates this association using a classic as well as emotional antisaccade paradigm to study inhibitory control performance. Ninety participants completed affective questionnaires (Beck Depression Inventory-II, and Mood Scale), a 6-minute baseline electrocardiogram, and two different antisaccade tasks. After the baseline, subjects were presented with a video sequence with either neutral, sad, or emotionally arousing content. By subtracting the baseline from the video sequence, we computed HRV reactivity and tested whether the reactivity score could predict inhibitory control performance. We hypothesized that this would be the case in both the sadness and arousal group, but not in the neutral one. Furthermore, we awaited significant performance differences between experimental groups. Contrary to our assumption, inhibitory control performance did not differ between experimental groups. Moreover, there was no significant relation between affective measures and task performance. Nevertheless, cardiovascular reactivity in terms of HRV was predictive of error rates in both antisaccade tasks in the sadness group. We could find this effect neither in the neutral nor in the arousal group. In addition, BDI scores moderated the effect in the emotional task. Results indicate that emotional reactivity to a sad video stimulus as indexed by HRV as well as the interaction with current emotional state predict inhibitory control performance.