The prevalence of hazardous drinking among females has increased more in the past decades as compared to among males. While it is well-known that females suffer more from the negative effects of alcohol use than males, the mechanisms that explain sex differences in hazardous drinking remain poorly understood. The current study aimed to investigate sex differences in the relationship between cue-induced (relief and reward) craving and cue-induced heart rate variability in a sample of hazardous drinkers. One hundred fourteen hazardous drinkers (61 females) underwent an alcohol cue-exposure paradigm consisting of exposure to alcohol-related pictures, personalized script imagery, and alcohol paraphernalia. Relief- and reward cravings were measured before and after exposure using the Desire for Alcohol Questionnaire. Heart Rate Variability was measured continuously during the exposure using an electrocardiograph. While there was a significant increase in both reward and relief craving following the alcohol exposure paradigm, these effects were not moderated by sex. Importantly, however, exposure to alcohol cues was associated with a stronger reduction in Heart Rate Variability among males compared to female hazardous drinkers. Lastly, exposure-related reduction in Heart Rate Variability was significantly stronger in individuals that reported more exposure-induced relief craving, but these effects were not moderated by sex. In summary, our findings suggest that while there were no sex differences in exposure-induced Heart Rate Variability, there was in exposure-induced craving. These findings may pave the way for developing sex-specific interventions specifically targeting Heart Rate Variability, including Heart Rate Variability biofeedback.