Cognitive and motor processes are essential for optimal athletic performance. Individuals trained in different skills and sports may have specialized cognitive abilities and motor strategies related to the characteristics of the activity and the effects of training and expertise. Most studies have investigated differences in motor-related cortical potential (MRCP) during self-paced tasks in athletes but not in stimulus-related tasks. The aim of the present study was to identify the differences in performance and MRCP between skilled and novice martial arts athletes during two different types of tasks: a sustained attention task and a transient attention task. Behavioral and electrophysiological data from twenty-two martial arts athletes were obtained while they performed a continuous performance task (CPT) to measure sustained attention and a cued continuous performance task (c-CPT) to measure transient attention. MRCP components were analyzed and compared between groups. Electrophysiological data in the CPT task indicated larger prefrontal positive activity and greater posterior negativity distribution prior to a motor response in the skilled athletes, while novices showed a significantly larger response-related P3 after a motor response in centro-parietal areas. A different effect occurred in the c-CPT task in which the novice athletes showed strong prefrontal positive activity before a motor response and a large response-related P3, while in skilled athletes, the prefrontal activity was absent. We propose that during the CPT, skilled athletes were able to allocate two different but related processes simultaneously according to CPT demand, which requires controlled attention and controlled motor responses. On the other hand, in the c-CPT, skilled athletes showed better cue facilitation, which permitted a major economy of resources and “automatic” or less controlled responses to relevant stimuli. In conclusion, the present data suggest that motor expertise enhances neural flexibility and allows better adaptation of cognitive control to the requested task.