Postflight orthostatic challenge (OC), resulting from blood pooling in lower extremities, is a major health concern among astronauts that fly long-duration missions. Additionally, astronauts undergo physical demanding tasks resulting in acute fatigue, which can affect performance. However, the effects of concurrent OC and acute physical fatigue on performance have not been adequately investigated. The purpose of this study was to determine the relationship between acute physical fatigue and cognitive function during OC. Sixteen healthy participants performed the mental arithmetic task and psychomotor tracking tasks in the absence and presence of a prior 1-hour physically fatiguing exercise, on separate days under OC (induced via lower body negative pressure). We recorded task performances on the cognitive tests and prefrontal cortex oxygenation using functional near-infrared spectroscopy, along with physiological and subjective responses. The introduction of the cognitive tasks during OC increased cerebral oxygenation; however, oxygenation decreased significantly with the cognitive tasks under the acute fatigue conditions, particularly during the tracking task and in males. These differences were accompanied by comparable task performances. The findings suggest that mental arithmetic is a more effective countermeasure than psychomotor tracking under acute physical fatigue during OC. Whereas females did not show a significant difference in cerebral oxygenation due to task, males did, suggesting that it may be important to consider gender differences when developing countermeasures against OC.