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The aim of this study is to investigate the glycemic profile, oxidative stress, and antioxidant capacity in athletes after 12 weeks of ubiquinone supplementation. It was a double-blinded, randomized, parallel, placebo-controlled study. Thirty-one well-trained college athletes were randomly assigned to ubiquinone (300 mg/d, <i>n</i> = 17) or placebo group (<i>n</i> = 14). The glycemic profile [fasting glucose, glycated hemoglobin (HbA1c), homeostatic model assessment-insulin resistance (HOMA-IR), quantitative insulin sensitivity check index (QUICKI)], plasma and erythrocyte malondialdehyde (MDA), total antioxidant capacity (TAC), and ubiquinone status were measured. After supplementation, the plasma ubiquinone concentration was significantly increased (<i>p</i> < 0.05) and the level of erythrocyte MDA was significantly lower in the ubiquinone group than in the placebo group (<i>p</i> < 0.01). There was a significant correlation between white blood cell (WBC) ubiquinone and glycemic parameters [HbA1c, <i>r</i> = −0.46, <i>p</i> < 0.05; HOMA-IR, <i>r</i> = −0.67, <i>p</i> < 0.01; QUICKI, <i>r</i> = 0.67, <i>p</i> < 0.01]. In addition, athletes with higher WBC ubiquinone level (≥0.5 nmol/g) showed higher erythrocyte TAC and QUICKI and lower HOMA-IR. In conclusion, we demonstrated that athletes may show a better antioxidant capacity with higher ubiquinone status after 12 weeks of supplementation, which may further improve glycemic control.