Exercise increases quality of life and lowers all-cause mortality, likely by preventing cardiovascular disease. Although the beneficial effects of exercise are linked with reductions in chronic inflammation, individual responses vary and factors that contribute to the anti-inflammatory effects of cardiovascular fitness remain largely undefined. We sought to investigate the role of fatty acids in the inverse relationship between inflammation and cardiovascular fitness. In this cross-sectional study using data from 435 participants in NHANES and linear regression models with CRP as the outcome, we observed significant negative interactions between VO2max and omega-3 polyunsaturated fatty acids (PUFAs) but not saturated, monounsaturated, or omega-6 PUFAs. When stratified by omega-3 PUFA tertiles, participants in the medium tertile, but not low tertile, show an enhanced negative association between VO2max and CRP, with a-32.0% difference (95% CI:-44.95,-15.9%) per 10mL/kg/min of VO2max. Exploratory factor analysis identified five unique dietary fatty acid (FA) profiles. The FA profile consisting predominantly of omega-3 PUFA had the strongest negative association for VO2max and CRP, with a-28.2% difference in CRP (95% CI:-43.4,-8.9) per 10mL/kg/min of VO2max. We also found that alpha-linolenic acid (ALA) and docosahexaenoic acid (DHA) enhanced the negative association between VO2max and CRP, suggesting that the anti-inflammatory response to VO2max capacity is associated with ALA and DHA levels. Males, Whites, and individuals with lower BMI were more sensitive to the effects of omega-3 PUFAs, while having high SFA levels attenuated the benefit. This study suggests that omega-3 PUFAs are effect modifiers for VO2max and CRP and that the anti-inflammatory benefits of increasing cardiovascular fitness are associated with omega-3 PUFAs.