Introduction: The 5-hydroxytryptamine 2C receptor (HTR2C) rs6318 polymorphism has been associated with increased sensitivity to stress. This study investigated whether the rs6318 genotype modified the cortisol response to endurance physical activity. Methods: The HTR2C SNP was genotyped in a population of agonistic cyclists, and salivary cortisol levels were measured before and after an endurance competition. Results and Conclusion: Salivary cortisol levels increased after the competition (from 20.72 ± 12.36 ng/mL to 33.80 ± 21.53 ng/mL; p = 3.189 × 10–5). rs6318 C carriers displayed higher baseline cortisol levels compared to G carriers (26.60 ± 9.35 ng/mL vs. 19.50 ± 12.63 ng/mL; p = 0.04). Baseline cortisol levels were able to predict the cortisol response to exercise (β = –0.846; p = 1.2 × 10–5). Although regression analysis did not identify an association between HTR2C genotype and change in cortisol levels, a secondary analysis in which the population was classified by median cortisol changes suggested that they might be weakly associated, thus warranting further investigation.