Considering the existing controversy over the possible role of acute antioxidant vitamins in reducing exercise-induced muscle damage (EIMD), this doubled-blind, randomized and controlled trial aimed to determine whether supplementation with vitamins C and E could mitigate the EIMD in endurance-trained runners (n = 18). The exercise protocol involved a warm-up followed by 6 to 8 bouts of 1 km running at 75% maximum heart rate (HRmax). Two hours before the exercise protocol, participants took the supplementation with vitamins or placebo, and immediately afterwards, blood lactate, rate of perceived exertion and performance were assessed. At 24 h post-exercise, CK, delayed onset muscle soreness and performance were determined (countermovement jump, squat jump and stiffness test). The elastic index and vertical stiffness were calculated using a stiffness test. Immediately after the exercise protocol, all participants showed improved maximum countermovement jump, which only persisted after 24 h in the vitamin group (p < 0.05). In both groups, squat jump height was significantly greater (p < 0.05) immediately after exercise and returned to baseline values after 24 h. The elastic index increased in the vitamin group (p < 0.05), but not in the placebo group. In both groups, lactate levels increased from pre- to immediately post-exercise (p < 0.05), and CK increased from pre- to 24 h post-exercise (p < 0.05). No significant differences between groups were observed in any of the variables (p > 0.05). Vitamin C and E supplementation does not seem to help with EIMD in endurance-trained individuals.