Previous studies have shown that polyphenol supplementation may be an effective strategy to improve exercise performance, due to their antioxidant character and ability to stimulate NO production. These properties may contribute to exercise performance, yet no conclusive research has been performed in exploring the direct effects of citrus flavonoids on human exercise performance. Therefore, the purpose of this study was to assess whether supplementation of a customized citrus flavonoid (CF) extract for 4 weeks improves cycling time-trial performance in trained male athletes. In a double-blind, randomized, parallel study, 39 healthy, trained males were given a daily dose of either 500 mg of a customized citrus flavonoid extract (CF) or a placebo for 4 weeks. Exercise performance was tested by means of a time-trial test on a cycle ergometer, during which participants had to generate as much power as possible for duration of 10 minutes. Absolute power output significantly increased with 14.9 ± 3.9 W after 4 weeks of CF supplementation, corresponding with a 5.0% increase, compared to 3.8 ± 3.2 W (1.3% increase) in placebo (p < 0.05). In addition, oxygen consumption/power ratio significantly decreased in the CF group compared to placebo (p = 0.001), and a trend was found in the change in peak power output in CF (18.2 ± 23.2 W) versus placebo (-28.4 ± 17.6 W; p = 0.116). The current study is the first convincing report that citrus flavonoid supplementation can improve exercise performance, as shown by a significant increase in power output during the exercise test.