This study investigated the long-term cardiovascular effects of coronavirus disease (COVID-19) in elite male athletes by comparing the heart rate variability (HRV), arterial stiffness, and other cardiovascular parameters between those with and without prior COVID-19 infection. Methods: This cross-sectional study evaluated 120 elite male athletes (60 post COVID-19, 60 controls) using anthropometric measurements, body composition analysis, pulmonary function tests, HRV analysis, arterial stiffness assessments, hemodynamic monitoring, and microcirculatory function tests. Results: Athletes post COVID-19 showed significantly higher lean mass (p = 0.007), forced vital capacity (p = 0.001), and forced expiratory volume in 1 s (p = 0.007) than controls. HRV parameters did not significantly differ between the groups. Post-COVID-19 athletes exhibited peripheral vascular resistance (p = 0.048) and reflection index (p = 0.038). No significant differences were observed in the blood pressure, cardiac output, oxygen saturation, or microcirculatory oxygen absorption. Conclusions: Elite male athletes showed notable cardiovascular resilience after COVID-19, with only minor differences in vascular function. The maintained cardiac autonomic function and improved lung parameters in post-COVID-19 athletes suggests an adaptive response. These findings support the cardiovascular health of elite athletes following COVID-19 but emphasize the importance of continued monitoring.