Purpose <p>Variation in fat mass and obesity-associated gene (<i>FTO</i>) is a critical risk factor in the etiology of obesity. <i>FTO</i> is associated with preference and sensory perception of nutrients and dietary intake. However, the effect of genetic variation on overall dietary quality has not yet been fully elucidated. This study examined whether <i>FTO</i> rs9939609 (T &gt; A) was associated with dietary quality in Koreans.</p> Methods <p>Data of 46,928 individuals from the Korean Genome and Epidemiology Study were analyzed according to <i>FTO</i> rs9939609 genotype, general characteristics, and diet quality based on the Korean Healthy Eating Index (KHEI), employing sex- and age-stratified approaches.</p> Results <p>The <i>FTO</i> genotype did not significantly influence overall diet quality; however, female carriers of the obesity risk allele A (TA + AA) showed significantly higher KHEI scores for balance of energy nutrient consumption, especially for carbohydrate ratio (2.00 ± 1.99 versus 1.90 ± 1.98, <i>P</i>_adjusted &lt;0.001) and fat ratio (2.87 ± 2.15 versus 2.76 ± 2.17, <i>P</i>_adjusted &lt;0.001) than A-allele non-carriers (TT). Furthermore, when the females were grouped based on their median age (51 years), such an association between the <i>FTO</i> genotype and energy nutrient ratio was only evident in the younger group. However, such an effect of the genetic variant on diet quality and energy nutrient consumption was not evident in males, and the interactive effect of <i>FTO</i> and sex and age was not statistically significant.</p> Conclusion <p>The <i>FTO</i> rs9939609 (T &gt; A) polymorphism is associated with dietary quality, particularly influencing the balance of energy nutrient intake in Korean females.</p>