The aim of this study was to analyze the cardiac autonomic function at rest, at maximum exercise, and in recovery after exercise and to determine sex-specific and age-specific values for resting heart rate (RHR), hear rate (HR)-peak, HR recovery (HRR), and HR variability at rest in master runners. Fifty endurance runners (21 women) participated in this study (43.28 ± 5.25 years). The subjects came from different athletic clubs in Andalusia (Spain), and the testing protocol was performed in-season. A 3-km running test was performed and the cardiovascular response was monitored. Regarding sex, no significant differences were found regarding cardiovascular autonomic function at rest, during exercise, and following maximal exercise, only at rest, the standard deviation of all R-R intervals and low frequency values displayed significantly (p < 0.05) lower scores in women. 46% of athletes showed an RHR < 60 bpm. Additionally, HR-peak showed a significant correlation with age (r = −0.369; p = 0.009) and HRR_5min (r = 0.476, p = 0.001). Also, endurance performance was inversely associated with obesity traits and cardiometabolic risk factors. In summary, age, sex, fitness, or anthropometrics characteristics did not show a relevant influence on cardiovascular autonomic modulation in master runners. However, the 3-km performance displayed a significant negative association with several factors of cardiometabolic risk.