Hypothyroidism may be associated with changes in the autonomic regulation of the cardiovascular system, which may have clinical implications. To conduct a systematic review and meta-analysis on the impact of hypothyroidism on HRV. PubMed, Cochrane, Embase and Google Scholar were searched until 20 August 2021 for articles reporting HRV parameters in untreated hypothyroidism and healthy controls. Random-effects meta-analysis were stratified by degree of hypothyroidism for each HRV parameters: RR intervals (or normal to normal-NN intervals), SDNN (standard deviation of RR intervals), RMSSD (square root of the mean difference of successive RR intervals), pNN50 (percentage of RR intervals with >50ms variation), total power (TP), LFnu (low-frequency normalized unit), HFnu (high-frequency), VLF (very low frequency), and LF/HF ratio. We included 17 studies with 11438 patients: 1163 hypothyroid patients and 10275 healthy controls. There was a decrease in SDNN (effect size = -1.27, 95% CI -1.72 to -0.83), RMSSD (-1.66, -2.32 to -1.00), pNN50 (-1.41, -1.98 to -0.84), TP (-1.55, -2.1 to -1.00), HFnu (-1.21, -1.78 to -0.63) with an increase in LFnu (1.14, 0.63 to 1.66) and LF/HF ratio (1.26, 0.71 to 1.81) (p <0.001). HRV alteration increased with severity of hypothyroidism. Hypothyroidism is associated with a decreased HRV, that may be explained by molecular mechanisms involving catecholamines and by the effect of TSH on HRV. The increased sympathetic and decreased parasympathetic activity may have clinical implications.