Heart rate variability (HRV) has been used to explore the parasympathetic activity of individuals with problematic Internet use (PIU), but the results are controversial. We conducted a systematic review and meta-analysis of studies comparing HRV in PIU individuals and healthy participants from several databases. HRV was analyzed according to the parasympathetic activity in hierarchical order (primary analysis), and the total variability (secondary analysis). The baseline HRV and HRV reactivity were both considered. Of the 106 studies screened, 12 were included in the quantitative analysis. Significant differences were observed for baseline HRV in PIU individuals compared to the controls. Regarding HRV reactivity, PIU individuals did not have a significantly lower HRV value during pleasant or unpleasant stimuli. In summary, PIU individuals and healthy subjects had significantly different resting state parasympathetic activity. The finding of HRV reactivity in PIU individuals awaits further investigation.