This research investigated the effects of music and its time of application on a 5-km run. Fifteen well-trained male long-distance runners (24.87 ± 2.47 years; 78.87 ± 10.57 kg; 178 ± 07 cm) participated in this study. Five randomized experimental conditions during a 5-km run on an official track were tested (PM: motivational songs, applied before 5 km of running; SM: slow motivational songs, applied during 5 km of running; FM: fast and motivational songs, applied during 5 km of running; CS: calm songs, applied after 5 km of running; CO: control condition). Psychophysiological assessments were performed before (functional near-infrared spectroscopy, heart rate variability [HRV], valence, and arousal), during (performance time, heart rate, and rate of perceived exertion [RPE]), and after (mood, RPE, and HRV) tests. The chosen songs were considered pleasurable and capable of activating. Furthermore, they activated the 3 assessed prefrontal cortex (PFC) areas (medial, right dorsolateral, and left dorsolateral) similarly, generating positive emotional consequences by autonomous system analysis. The first 800 m was accomplished faster for SM and FM compared with other conditions (p ≤ 0.05); moreover, there was a high probability of improving running performance when music was applied (SM: 89%; FM: 85%; PM: 39%). Finally, music was capable of accelerating vagal tonus after 5 km of running with CS (p ≤ 0.05). In conclusion, music was able to activate the PFC area, minimize perceptions, improve performance, and accelerate recovery during 5 km of running.