The extent to which post-exercise cardiac autonomic control depends on exercise modality remains unclear, particularly among individuals with autonomic dysfunction (CAdysf). This study compared heart rate variability (HRV) and baroreflex sensitivity (BRS) responses to acute aerobic (AE) and strength exercise (SE) in men with CAdysf. Twenty men were assigned into control (n=10: 33.8±3.0 yr; 23.7±1.5 kg/m2) and CAdysf (n=10: 36.2±9.8 yr; 28.4±2.6 kg/m2) groups. CAdysf underwent AE, SE, and a non-exercise control day (CTL) in a randomized, counter-balanced order. HRV and BRS were assessed in a supine position during 25-min of recovery after AE, SE, and CTL. Both HRV indices [P < 0.05; Effect size (Cohen's d): > 1.4] and BRS at rest were significantly lower in CAdysf than controls [P < 0.01; Effect size (Cohen's d): ≥ 1.36]. In CAdysf, post-exercise increases in heart rate, sympathetic activity (low-frequency band, LF), and sympathovagal balance (LF:HF ratio), as well as decreases in R-R interval, parasympathetic activity (high-frequency band, HF), and BRS were observed in AE [P < 0.05; Effect size (Cohen's d): ≥ 1.31] and SE [P < 0.05; Effect size (Cohen's d): ≥ 0.79] vs. CTL, but changes were larger after AE than SE [P < 0.05; Effect size (Cohen's d): ≥ 0.73]. In conclusion, both AE and SE elicited post-exercise changes in HRV and BRS among CAdysf men, primarily reflected by lowered vagal modulation, increased sympathovagal balance, and a delayed BRS recovery pattern. However, those changes seem to be more likely to occur after AE than SE.