Background: Our aim was to determine the impact that metabolic syndrome (MS) produces in long-term heart rate variability (HRV), quantitatively synthesizing the results of published studies to characterize the cardiac autonomic dysfunction in MS. Methods: We searched electronic databases for original research works with long-term HRV recordings (24 h) that compared people with MS (MS+) versus healthy people as a control group (MS−). This systematic review and meta-analysis (MA) was performed according to PRISMA guidelines and registered at PROSPERO (CRD42022358975). Results: A total of 13 articles were included in the qualitative synthesis, and 7 of them met the required criteria to be included in the MA. SDNN (−0.33 [−0.57, 0.09],p= 0.008), LF (−0.32 [−0.41, −0.23],p< 0.00001), VLF (−0.21 [−0.31, −0.10],p= 0.0001) and TP (−0.20 [−0.33, −0.07],p= 0.002) decreased in patients with MS. The rMSSD (p= 0.41), HF (p= 0.06) and LF/HF ratio (p= 0.64) were not modified. Conclusions: In long-term recordings (24 h), SDNN, LF, VLF and TP were consistently decreased in patients with MS. Other parameters that could be included in the quantitative analysis were not modified in MS+ patients (rMSSD, HF, ratio LF/HF). Regarding non-linear analyses, the results are not conclusive due to the low number of datasets found, which prevented us from conducting an MA.