This study investigated the effects of acute hypoxic exposure on post-exercise cardiac autonomic modulation following maximal cardiopulmonary exercise testing (CPET). Thirteen healthy men performed CPET and recovery in normoxia (N) and normobaric hypoxia (H) (FiO2 = 13.4%, ≈ 3500m). Post-exercise cardiac autonomic modulation was assessed during recovery (300s) through the analysis of fast-phase and slow-phase heart rate recovery (HRR) and heart rate variability (HRV) indices. Both short-term, T30 (mean difference (MD) 60.0s, 95% CI 18.2-101.8, p = 0.009, ES 1.01), and long-term, HRRt (MD 21.7s, 95% CI 4.1-39.3, p = 0.020, ES 0.64), time constants of HRR were higher in H. Fast-phase (30 and 60s) and slow-phase (300s) HRR indices were reduced in H either when expressed in bpm or in percentage of HRpeak (p < 0.05). Chronotropic reserve recovery was lower in H than in N at 30s (MD - 3.77%, 95% CI - 7.06 to - 0.49, p = 0.028, ES - 0.80) and at 60s (MD - 7.23%, 95% CI - 11.45 to - 3.01, p = 0.003, ES - 0.81), but not at 300s (p = 0.436). Concurrently, Ln-RMSSD was reduced in H at 60 and 90s (p < 0.01) but not at other time points during recovery (p > 0.05). Affected fast-phase, slow-phase HRR and HRV indices suggested delayed parasympathetic reactivation and sympathetic withdrawal after maximal exercise in hypoxia. However, a similar cardiac autonomic recovery was re-established within 5min after exercise cessation. These findings have several implications in cardiac autonomic recovery interpretation and in HR assessment in response to high-intensity hypoxic exercise.