Introduction The link between dietary fats and obesity is still controversial, as in Western diets the percentage of energy from total fat has decreased while the intake of omega-6 has increased, and omega-3 decreased. These changes have corresponded with a significant increase in the prevalence of obesity. Objective This study aims to examine the association of percentages of energy intake (EI) from omega-3 and omega-6 and Σω-6/Σω-3 ratio with BMI and two proxy indicators of central obesity (waist circumference [WC], waist-to-height ratio [WHtR]) and relative fat mass (RFM) estimator of whole-body fat. Design A representative sample of 3,733 adults was used from the UK National Diet and Nutrition Survey Rolling Programme (2008/09-2018/19). An estimated four-day food record was used to calculate dietary intake. Regression models were used to verify the association of omega-3 and omega-6 and quintiles of Σω-6/ Σω-3 ratio with general and abdominal obesity with adjustment for important confounders. A p-value of <0.05 represented statistical significance. Results The findings of this study show that the average ratio of Σω-6/Σω-3 was 5.5:1 ± 2. There was a significant association between the ratio of Σω-6/Σω-3 and BMI, WC, WHtR and RFM. However, the percentage of total EI from total fat was only significant with BMI, while the percentage of EI from omega-3 was negatively associated with WC, WHtR and RFM. No association was found between the percentage of EI from omega-6 and general or abdominal obesity. Conclusion The effect of Σω-6/Σω-3 may be largely driven by a deficiency in the intake of omega-3. Omega-6 and omega-3 should be listed as such in national surveys instead of polyunsaturated fatty acid (PUFA). Meeting recommended levels of omega-3 and lowering Σω-6/Σω-3 are imperative to establish healthier dietary patterns and prevent obesity.