Objectives Short-sleep is becoming increasingly common and may negatively affect brain function including cognitive ability. Physical exercise has been proved to improve cognitive function while intensity matters. This study was conducted to examine the effects of 12-week exercise interventions on cognitive performance and prefrontal cortex activation related to task performance in short-sleep young adults. Methods A total of 50 subjects (23.62 ± 5.28 years and 24 men) with regular short-sleep conditions (textless7 h per night) participated in this study and were divided into three groups: control, moderate-intensity continuous training (MICT), and high-intensity interval training (HIIT) group. As task performance (congruent and incongruent Stroop) was monitored, changes in prefrontal oxygenated hemoglobin (oxyHb), an indicator of cortical activation, were measured using functional near-infrared spectroscopy (fNIRS) to explore the hemodynamics mechanism. Results Post 12-week intervention, significant differences in reaction time for congruent [β (95%CI): −0.045 (−0.088, −0.002), p = 0.039] and incongruent Stroop tests [β (95%CI): −0.058 (−0.113, −0.003), p = 0.038] were found only in the MICT intervention group. However, HIIT did not show significant improvements in cognitive function. Left middle frontal gyrus (Frontal Mid L) and right dorsolateral superior frontal gyrus (Frontal Sup R) were both stimulated by MICT and HIIT. Moreover, left dorsolateral superior frontal gyrus (Frontal Sup L) was stimulated by MICT. Conclusion The findings indicated that 12-week MICT improved cognition by significantly increasing cortical activity across more brain regions. Thus, we suggested that maintaining moderate-intensity exercise could benefit cognitive function despite short sleep.