Purpose: Although exercise and sleep duration habits are associated with cognitive function, their beneficial effects on cognitive function remain unclear. We aimed to examine the effect of sleep duration and daily physical activity on cognitive function, elucidating the neural mechanisms using near-infrared spectroscopy (NIRS). Methods: A total of 23 healthy young adults (age 22.0 ± 2.2 years) participated in this study. Exercise amount was assessed using a uniaxial accelerometer. We evaluated total sleep time (TST) and sleep efficiency by actigraphy. Cognitive function was tested using the N-back task, the Wisconsin Card Sorting Test (WCST), and the Continuous Performance Test-Identical Pairs (CPT-IP), and the cortical oxygenated hemoglobin levels during a word fluency task were measured with NIRS. Results: Exercise amount was significantly correlated with reaction time on 0- and 1-back tasks (r = -0.602, p = 0.002; r = -0.446, p = 0.033, respectively), whereas TST was significantly correlated with % corrects on the 2-back task (r = 0.486, p = 0.019). Multiple regression analysis, including exercise amount, TST, and sleep efficiency, revealed that exercise amount was the most significant factor for reaction time on 0- and 1-back tasks (β = -0.634, p = 0.002; β = -0.454, p = 0.031, respectively), and TST was the most significant factor for % corrects on the 2-back task (β = 0.542, p = 0.014). The parameter measured by WCST and CPT-IP was not significantly correlated with TST or exercise amount. Exercise amount, but not TST, was significantly correlated with the mean area under the NIRS curve in the prefrontal area (r = 0.492, p = 0.017). Conclusion: Exercise amount and TST had differential effects on working memory and cortical activation in the prefrontal area. Daily physical activity and appropriate sleep duration may play an important role in working memory.