Background and Objectives: The available research shows conflicting data on the heart rate variability (HRV) in metabolic syndrome (MetS) subjects. The discrepancy suggests a methodical shortcoming: due to the influence of physical activity, the standard measuring of HRV at rest is not comparable with HRV assessment based on 24 h Holter monitoring, which is preferred because of its comprehensiveness. To obtain a more reliable measure and to clarify to what extent HRV is altered in MetS, we assessed a 24 h HRV before and after the elimination of the influence of physical activity. Materials and Methods: We investigated 69 metabolic syndrome (MetS) and 37 control subjects, aged 50–55. In all subjects, 24 h monitoring of electrocardiogram, blood pressure, and actigraphy profiles were conducted. To eliminate the influence of day-time physical activity on RR intervals (RRI), a linear polynomial autoregressive model with exogenous terms (ARX) was used. Standard spectral RRI analysis was performed. Results: Subjects with MetS had blunted HRV; the diurnal SDNN index was reliably lower in the MetS group than in control subjects. The elimination of the influence of physical activity did not reveal a significant HRV change in long-term indices (SDNN, SDANN, and SD2), whilst adjacent RRI values (RMSSD, pNN50, and SD1) and SDNN index significantly increased (p < 0.001). An increase in the latter indices highlighted the HRV difference between the MetS and control groups; a significant (p < 0.001) decrease of all short-term HRV variables was found in the MetS group (p < 0.01), and low-frequency spectral components were less pronounced in the MetS group. Conclusion: The application of a polynomial autoregressive model in 24 h HRV assessment allowed for the exclusion of the influence of physical activity and revealed that MetS is associated with blunted HRV, which reflects mitigated parasympathetic tone.