Abstract: The purpose of this study was to examine how two common methods of continuous hypoxaemia impact the activity of intracortical circuits responsible for inhibition and facilitation of motor output, and spinal excitability. Ten participants were exposed to 2 h of hypoxaemia at 0.13 fraction of inspired oxygen ((Figure presented.) clamping protocol) and 80% of peripheral capillary oxygen saturation ((Figure presented.) clamping protocol) using a simulating altitude device on two visits separated by a week. Using transcranial magnetic and peripheral nerve stimulation, unconditioned motor evoked potential (MEP) area, short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF), and F-wave persistence and area were assessed in the first dorsal interosseous (FDI) muscle before titration, after 1 and 2 h of hypoxic exposure, and at reoxygenation. The clamping protocols resulted in differing reductions in (Figure presented.) by 2 h ((Figure presented.) clamping protocol: 81.9 ± 1.3%, (Figure presented.) clamping protocol: 90.6 ± 2.5%). Although unconditioned MEP peak to peak amplitude and area did not differ between the protocols, SICI during (Figure presented.) clamping was significantly lower at 2 h compared to (Figure presented.) clamping (P = 0.011) and baseline (P < 0.001), whereas ICF was higher throughout the (Figure presented.) clamping compared to (Figure presented.) clamping (P = 0.005). Furthermore, a negative correlation between SICI and (Figure presented.) (r rm = −0.56, P = 0.002) and a positive correlation between ICF and (Figure presented.) (r rm = 0.69, P = 0.001) were determined, where greater reductions in (Figure presented.) correlated with less inhibition and less facilitation of MEP responses. Although F-wave area progressively increased similarly throughout the protocols (P = 0.037), persistence of responses was reduced at 2 h and reoxygenation (P < 0.01) during the (Figure presented.) clamping protocol compared to the (Figure presented.) clamping protocol. After 2 h of hypoxic exposure, there is a reduction in the activity of intracortical circuits responsible for inhibiting motor output, as well as excitability of spinal motoneurones. However, these effects can be influenced by other physiological responses to hypoxia (i.e., hyperventilation and hypocapnia). New Findings: What is the central question of this study? How do two common methods of acute hypoxic exposure influence the excitability of intracortical networks and spinal circuits responsible for motor output? What is the main finding and its importance? The excitability of spinal circuits and intracortical networks responsible for inhibition of motor output was reduced during severe acute exposure to hypoxia at 2 h, but this was not seen during less severe exposure. This provides insight into the potential cause of variance seen in motor evoked potential responses to transcranial magnetic stimulation (corticospinal excitability measures) when exposed to hypoxia.