The aim of this study was to determine the influence of the CYP1A2 c.-163A > C (rs762551) polymorphism on the effect of oral caffeine intake on fat oxidation during exercise. Using a pilot randomized, double-blind, crossover, placebo-controlled trial, 32 young and healthy individuals (women = 14, men = 18) performed an incremental test on a cycle ergometer with 3-min stages at workloads from 30 to 70% of maximal oxygen uptake (VO2max). Participants performed this test after the ingestion of (a) placebo; (b) 3mg/kg of caffeine; (c) 6mg/kg of caffeine. Fat oxidation rate during exercise was measured by indirect calorimetry. The influence of the CYP1A2 c.-163A > C polymorphism in the effect of caffeine on fat oxidation rates during exercise was established with a three-way ANOVA (substance × genotype × intensity). Eight participants were genotyped as AA, 18 participants were CA heterozygotes, and 6 participants were CC. There was a main effect of substance (F = 3.348, p = 0.050) on fat oxidation rates during exercise with no genotype effect (F = 0.158, p = 0.959). The post hoc analysis revealed that, in comparison to the placebo, 3 and 6mg/kg of caffeine increased fat oxidation at 40-50% VO2max in AA (all p < 0.050) and 50-60% VO2max in CA and CC participants (all p < 0.050). Oral intake of 3 and 6mg/kg of caffeine increased fat oxidation rate during aerobic exercise in individuals with AA, CA and CC genotypes. This suggests that the effect of caffeine to enhance fat oxidation during exercise is not influenced by the CYP1A2 c.-163A > C polymorphism. The study was registered on clinicaltrials.gov with ID: NCT05975489.