Metabolic syndrome (MetS) represents a cluster of metabolic abnormalities that include hypertension, central obesity, insulin resistance, and dyslipidemia and is strongly associated with an increased risk of diabetes, cardiovascular diseases (CVD), and all-cause mortality. Early diagnosis is important to employ lifestyle and risk factor modification. Existing therapies are limited. Studies report positive effect of omega-3 fatty acids (ω-3FA) on symptoms of metabolic syndrome. The present study was undertaken to evaluate the effect of ω-3FA alone and in combination with proprietary chromium complex (PCC) on endothelial function in subjects with metabolic syndrome. In this randomized, double-blind, parallel-group study, subjects were enrolled into the study after ethics committee (EC) approval and informed consent. Eligible subjects were randomized to receive ω-3FA concentrate 2000 mg (Group A-18 subjects), ω-3FA concentrate 2000 mg + PCC200 mcg (Group B-19 subjects), and ω-3FA concentrate 2000 mg + PCC400 mcg (Group C-21 subjects) daily for 12 weeks. Endothelial dysfunction as measured by reflection index (RI), biomarkers of oxidative stress (NO, MDA, and glutathione), and inflammation (hsCRP, endothelin-1, ICAM-1, and VCAM-1) were evaluated at baseline, 4, and 12 weeks. Lipid-profile and platelet-aggregation tests were performed at baseline and 12 weeks. Adverse drug reactions were recorded. Compliance was assessed by pill count method. GraphPad Prism8 was used for statistical analysis. Significant changes were seen from 4 weeks onwards in all the parameters evaluated. Significant improvement in RI% (mean ± SD = −2.56 ± 0.77 to −3.27 ± 0.67-group A, −2.33 ± 0.76 to 4.72 ± 0.79-group B; −2.39 ± 1.13 to 6.46 ± 1.00-group C) was seen at 12 weeks. Significant improvement in biomarkers of oxidative stress and inflammation was seen with all the treatment groups. Similarly, significant improvement in lipid profile was seen in group B and group C, while group A showed change in HDL, VLDL, and TG. Group C demonstrated the best response in the parameters evaluated. Three patients in group C reported gastrointestinal adverse events, which resolved spontaneously; none stopped the therapy. So, the addition of PCC to ω-3FA may prove to have beneficial effect in reducing cardiovascular morbidity in MetS patients.