Cerebral and skeletal muscle oxygenation are critical research areas for understanding blood flow and oxygen delivery during various physiological states, including cognitive tasks and exercise. Measuring oxygenated and deoxygenated hemoglobin through functional near-infrared spectrometry (fNIRS) enables non-invasive assessment of cerebral and skeletal muscle oxygenation. Research using fNIRS to explore oxygenation after sleep deprivation (SD) is limited and often contradictory. We reviewed how SD affects cerebral and muscle oxygenation as part of a broader review of how SD affects exercise through altered physiologic and perceptual responses. Herein, we consolidate existing knowledge, identify gaps, and suggest directions for future investigation. A comprehensive literature review was conducted via predefined search parameters using PubMed and Google Scholar, focusing on studies that employed fNIRS to measure cerebral and/or skeletal muscle oxygenation in humans after SD (total or partial) or in individuals with chronically fragmented sleep due to obstructive sleep apnea (OSA). Select studies report increased cerebral oxygenation post-SD, potentially due to compensatory mechanisms and increased brain activity. Contrarily, several studies indicate decreased cerebral oxygenation following SD, potentially due to impaired endothelial function, cortical neurovascular coupling, suppressed brain activity, or decreased oxygen consumption. Cerebral oxygenation may be associated with perceived exertion, suggesting meaningful links to exercise. Interestingly, exercise training may mitigate the effects of SD on oxygenation. The only study investigating skeletal muscle oxygenation with regards to sleep status found a lower tissue saturation index in OSA participants compared to controls, though hemoglobin parameters did not differ. The effect of SD on oxygenation remains equivocal, with no studies fully elucidating the mechanisms underlying these changes. This review is the foundation for an ongoing prospective study investigating the impact of acute SD on exercise capacity and fNIRS-derived cerebral and skeletal muscle oxygenation, with two participants enrolled to date and interim analyses planned at n=5 participants.