The study aimed to evaluate the changes of nicotinamide adenine dinucleotide (NADH) fluorescence in the reduced form in the superficial skin layer, resulting from a 7-week training period in highly trained competitive athletes (n = 41). The newly, non-invasive flow mediated skin fluorescence (FMSF) method was implemented to indirectly evaluate the mitochondrial activity by NADH fluorescence. The FMSF measurements were taken before and after an exercise treadmill test until exhaustion. We found that athletes showed higher post-training values in basal NADH fluorescence (pre-exercise: 41% increase; post-exercise: 49% increase). Maximum NADH fluorescence was also higher after training both pre- (42% increase) and post-exercise (47% increase). Similar changes have been revealed before and after exercise for minimal NADH fluorescence (before exercise: 39% increase; after exercise: 47% increase). In conclusion, physical training results in an increase in the skin NADH fluorescence levels at rest and after exercise in athletes.