Altered autonomic function has been identified following ultra-endurance event participation among elite world-class athletes. Despite dramatic increases in recreational athlete participation in these ultra-endurance events, the physiological effects on these athletes are less known. This investigation sought to characterise changes in surrogate measures of autonomic function: heart rate variability (HRV), blood pressure variability (BPV) and baroreceptor sensitivity (BRS) following ultra-endurance race participation. Further, we sought to compare baseline measures among ultra-endurance athletes and recreationally active controls not participating in the ultra-endurance race. Recreational ultra-endurance athletes (n = 25, 44.6 ± 8.2 years, 8 females) and recreationally active age, sex and body mass index matched controls (n = 25) were evaluated. Measurements of HRV, BPV and BRS were collected pre- and post-race for recreational ultra-endurance athletes and at baseline, for recreationally active controls. Post-race, ultra-endurance athletes demonstrated significantly greater sympathetic modulation [low frequency (LF) power HRV: 50.3 ± 21.6 normalised units (n.u.) to 65.9 ± 20.4 n.u., p = 0.01] and significantly lower parasympathetic modulation [high frequency (HF) power HRV: 45.0 ± 22.4 n.u. to 23.9 ± 13.1 n.u., p < 0.001] and BRS. Baseline measurements BRS (spectral: 13.96 ± 10.82 ms·mmHg(-1) vs. 11.39 ± 5.33 ms·mmHg(-1)) were similar among recreational ultra-endurance athletes and recreationally active controls, though recreational ultra-endurance athletes demonstrated greater parasympathetic modulation of some HRV and BPV measures. Recreational ultra-endurance athletes experienced increased sympathetic tone and declines in BRS post-race, similar to previously reported elite world-class ultra-endurance athletes, though still within normal population ranges.