Chlorogenic acids (CGAs) reduce blood pressure and body fat, and enhance fat metabolism. In roasted coffee, CGAs exist together with the oxidant component hydroxyhydroquinone (HHQ). HHQ counteracts the antihypertensive effects of CGA, but its effects on CGA-induced fat oxidation (FOX) are unknown. Here we assessed the effects of CGA-enriched and HHQ-reduced coffee on FOX. Fifteen healthy male volunteers (age: 38 ± 8 years (mean ± SD); BMI: 22.4 ± 1.5 kg/m²) participated in this crossover study. Subjects consumed the test beverage (coffee) containing the same amount of CGA with HHQ (CGA-HHQ(+)) or without HHQ (CGA-HHQ(−)) for four weeks. Postprandial FOX and the ratio of the biological antioxidant potential (BAP) to the derivatives of reactive oxygen metabolites (d-ROMs) as an indicator of oxidative stress were assessed. After the four-week intervention, postprandial FOX and the postprandial BAP/d-ROMs ratio were significantly higher in the CGA-HHQ(−) group compared with the CGA-HHQ(+) group (4 ± 23 mg/min, group effect: p = 0.040; 0.27 ± 0.74, group effect: p = 0.007, respectively). In conclusion, reducing the amount of HHQ facilitated the postprandial FOX effects of CGA in coffee. Our findings also suggest that the mechanism underlying the inhibition of FOX by HHQ is related to postprandial oxidative stress.