•Mental stress significantly reduced variability and chaotic behaviour of HRV.•Stress causes sympathetic activation and parasympathetic withdrawal.•Pooled HRV power ratio changed significantly while did not in individual studies.•Studies investigating HRV non-linear measures and mental stress are required.•The method proposed to meta-analyze HRV features can be adopted for other studies investigating HRV. Mental stress reduces performances, on the work place and in daily life, and is one of the first causes of cognitive dysfunctions, cardiovascular disorders and depression. This study systematically reviewed existing literature investigating, in healthy subjects, the associations between acute mental stress and short term Heart Rate Variability (HRV) measures in time, frequency and non-linear domain. The goal of this study was to provide reliable information about the trends and the pivot values of HRV measures during mental stress. A systematic review and meta-analysis of the evidence was conducted, performing an exhaustive research of electronic repositories and linear researching references of papers responding to the inclusion criteria. After removing duplicates and not pertinent papers, journal papers describing well-designed studies that analyzed rigorously HRV were included if analyzed the same population of healthy subjects at rest and during mental stress. 12 papers were shortlisted, enrolling overall 758 volunteers and investigating 22 different HRV measures, 9 of which reported by at least 2 studies and therefore meta-analyzed in this review. Four measures in time and non-linear domains, associated with a normal degree of HRV variations resulted significantly depressed during stress. The power of HRV fluctuations at high frequencies was significantly depressed during stress, while the ratio between low and high frequency resulted significantly increased, suggesting a sympathetic activation and a parasympathetic withdrawal during acute mental stress. Finally, among the 15 non-linear measures extracted, only 2 were reported by at least 2 studies, therefore pooled, and only one resulted significantly depressed, suggesting a reduced chaotic behaviour during mental stress. HRV resulted significantly depressed during mental stress, showing a reduced variability and less chaotic behaviour. The pooled frequency domain measures demonstrated a significant autonomic balance shift during acute mental stress towards the sympathetic activation and the parasympathetic withdrawal. Pivot values for the pooled mean differences of HRV measures are provided. Further studies investigating HRV non-linear measures during mental stress are still required. However, the method proposed to transform and then meta-analyze the HRV measures can be applied to other fields where HRV proved to be clinically significant.