Background The relationship between physical activity and cognitive functions is well established, with regular exercise improving cognitive functions. However, there is less clarity surrounding the effect of exercise-induced fatigue on attention network particularly in those with a history of continuous physical activity. Aims This research was aimed to determine whether exercise-induced fatigue can affect cognitive functions, especially those involved in attentional control (i.e., alerting, orientation, and executive functions) and to identify any differences in attentional control between active and inactive individuals after exercise-induced fatigue. Methods We compared the performance of 24 physically active and inactive participants in the Attentional Network Task, which allows for the assessment of the executive, orienting and alerting networks. Under two conditions regarding exercise-induced fatigue (pre-fatigue and post-fatigue), we used sub-maximum aerobic endurance training to induce fatigue to the exhaustion point. Results The results showed that fatiguing exercise improved alertness in both groups; however, the executive control network of the active group improved while the orienting and executive control networks of the inactive group performed worse. Conclusions Depending on the participants' degree of physical activity and the particular task used to test each of these attention networks, exercise-induced exhaustion had a different impact on different attention networks.