INTRODUCTION: Hypothyroidism may be associated with changes in the autonomic regulation of the cardiovascular system, which may have clinical implications. OBJECTIVE: To conduct a systematic review and meta-analysis on the impact of hypothyroidism on HRV. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.