Background: Our aim was to determine the differences in short-term heart rate variability (HRV) between patients with metabolic syndrome (MS) and healthy controls. Methods: We searched electronic databases for primary works with short-term HRV recordings (≤30 min) that made comparisons between individuals with MS versus healthy controls. This systematic review and meta-analysis (MA) was performed according to PRISMA guidelines and registered at PROSPERO (CRD42022358975). Results: Twenty-eight articles were included in the qualitative synthesis and nineteen met the criteria for the MA. Patients with MS showed decreased SDNN (−0.36 [−0.44, −0.28], p < 0.001), rMSSD (−7.59 [−9.98, −5.19], p < 0.001), HF (−0.36 [−0.51, −0.20], p < 0.00001) and LF (−0.24 [−0.38, −0.1], p = 0.001). In subsequent subanalyses, we found a decrease in SDNN (−0.99 (−1.45, −0.52], p < 0.001), rMSSD (−10.18 [−16.85, −3.52], p < 0.01) and HF (−1.04 [−1.97, −0.1] p < 0.05) in women. In men, only LF showed a significant lower value (−0.26 [−0.5, −0.02], p < 0.05). We could not perform MA for non-linear variables. Conclusions: Patients with MS showed changes in time-domain analyses, with lower values in SDNN and rMSSD. Regarding frequency-domain analyses, MS patients showed a decrease in HF and LF When sex was used as a grouping variable, the MA was only possible in one of both sexes (men or women) in rMSSD and LF/HF. Lastly, when data for both men and women were available, subanalyses showed a different behavior compared to mixed analyses for SDNN, HF and LF, which might point towards a different impact of MS in men and women.