Heart rate variability (HRV) is a non-invasive measure of cardiac autonomic function. A clearer understanding as to whether resting autonomic function represented by HRV could be associated with changes in peak exercise cardiac function remains unanswered. This study evaluated the effect of age and sex on HRV, cardiometabolic function, and determined the correlation between HRV and cardiac function in healthy individuals. Sixty-eight participants (age range: 19–78 years old, females, n = 28) were recruited. Participants were stratified according to age (younger (<40 years old, n = 43, females, n = 17) and older age groups (>55 years old, n = 25, females, n = 11). Firstly, HRV was measured using non-invasive impedance cardiography method (TaskForce, CNSystems, Graz, Austria) and recorded at rest (supine position) for 30 min. HRV measures included: low frequency (LF) power, high frequency (HF) power (both normalised (nu) and absolute units (ms2)) and LF/HF ratio. Participants then completed a progressive cardiorespiratory exercise test using a semi-recumbent cycle ergometer (Corival, Lode, Groningen, Netherlands) with simultaneous gas exchange measurements (Metalyzer 3B, Cortex, Leipzig, Germany). Cardiac function was represented by peak exercise cardiac power output index (CPO). After controlling for body mass index and physical activity, males had significantly higher mean vales of RR interval than females (males = 1043 ± 165; females = 952 ± 128 ms, p = 0.02). There was no significant main effect of age, sex or their interaction on any of the other HRV measures. In younger and older females, resting RR interval had a significant relationship with peak exercise CPO (young females: r = 0.54, p < 0.05; old females: r = 0.81, p < 0.01). There was also a significant relationship between resting HF power and peak exercise CPO in younger females (r = 0.70, p < 0.01). HRV was not influenced by age but RR interval was associated with peak exercise CPO in females regardless of age, whilst HF power was significantly associated with CPO in younger females only.