Military aviators endure high cognitive loads and hypoxic environments during flight operations, impacting the autonomic nervous system (ANS). The synergistic effects of these exposures on the ANS, however, are less clear. This study investigated the simultaneous effects of mild hypoxia and high cognitive load on the ANS in military personnel. This study employed a two-factor experimental design. Twenty-four healthy participants aged between 19 and 45 years were exposed to mild hypoxia (14.0% O2), normoxia (21.0% O2), and hyperoxia (33.0% O2). During each epoch (n = 5), participants continuously performed one 15 min and one 10 min series of simulated, in-flight tasks separated by 1 min of rest. Exposure sequences (hypoxia–normoxia and normoxia–hyperoxia) were separated by a 60 min break. Heart rate (HR), heart rate variability (HRV), and O2 saturation (SpO2) were continuously measured via an armband monitor (Warfighter MonitorTM, Tiger Tech Solutions, Inc., Miami, FL, USA). Paired and independent t-tests were used to evaluate differences in HR, HRV, and SpO2 within and between exposure sequences. Survival analyses were performed to assess the timing and magnitude of the ANS responses. Sympathetic nervous system (SNS) activity during hypoxia was highest in epoch 1 (HR: +6.9 bpm, p = 0.002; rMSSD: −9.7 ms, p = 0.003; SDNN: −11.3 ms, p = 0.003; SpO2: −8.4%, p < 0.0000) and appeared to slightly decline with non-significant increases in HRV. During normoxia, SNS activity was heightened, albeit non-significantly, in epoch 1, with higher HR (68.5 bpm vs. 73.0 bpm, p = 0.06), lower HRV (rMSSD: 45.1 ms vs. 38.7 ms, p = 0.09 and SDNN: 52.5 ms vs. 45.1 ms, p = 0.08), and lower SpO2 (−0.7% p = 0.05). In epochs 2–4, HR, HRV, and SpO2 trended towards baseline values. Significant between-group differences in HR, HRV, and O2 saturation were observed. Hypoxia elicited significantly greater HRs (+5.0, p = 0.03), lower rMSSD (−7.1, p = 0.03), lower SDNN (−8.2, p = 0.03), and lower SpO2 (−1.4%, p = 0.002) compared to normoxia. Hyperoxia appeared to augment the parasympathetic reactivation reflected by significantly lower HR, in addition to higher HRV and O2 relative to normoxia. Hypoxia induced a greater ANS response in military personnel during the simultaneous exposure to high cognitive load. The significant and differential ANS responses to varying O2 levels and high cognitive load observed highlight the importance of continuously monitoring multiple physiological parameters during flight operations.