The FTO rs9939609 gene, which presents three polymorphisms (AA, AT, and TT), has been associated with the development of obesity through an increased fat accumulation; however, the associations of the gene with other physiological mechanisms, such as appetite or fat oxidation, are still unclear. Therefore, this study aims to evaluate the influence of the FTO rs9939609 gene on different obesity-related factors in young adults. The FTO rs9939609 polymorphism was genotyped in 73 participants (28 women, 22.27 ± 3.70 years). Obesity-related factors included dietary assessment, physical activity expenditure, body composition, appetite sensation, resting metabolic rate, maximal fat oxidation during exercise (MFO), and cardiorespiratory fitness. Our results showed that TT allele participants expressed higher values of hunger (p = 0.049) and appetite (p = 0.043) after exercising compared to the AT allele group. Moreover, the TT allele group showed significantly higher values of MFO (p = 0.031) compared to the AT group, regardless of sex and body mass index. Thus, our results suggest that the FTO rs9939609 gene has an influence on appetite, hunger, and fat oxidation during exercise, with TT allele participants showing significantly higher values compared to the AT allele group. These findings may have practical applications for weight loss and exercise programs.