Analytical methodology for direct investigation of antioxidant systems continues to be a pressing research area. Consumer demand for natural products requires an increase in natural antioxidants; thus, fast, high-throughput, and cost-effective screening methods are in demand. In this study, square-wave voltammetry and gas chromatography with flame ionization detection (GC-FID) were used in conjunction to monitor antioxidant and fatty acid degradation, respectively, during the accelerated degradation of an omega-3 fatty acid sample. Butylated hydroxytoluene, sesamol, and rosemary extract were investigated as antioxidants. It was determined that voltammetry could be used to monitor the reduction in oxidation current, which provides a direct assessment method for the reduction of native antioxidant concentration throughout the accelerated degradation. Furthermore, results showed that voltammetry could be used to monitor fatty acid degradation similarly to the fatty acid methyl ester analysis routinely performed using gas chromatography separation. Both voltammetry and GC-FID methods reached similar conclusions about antioxidant quality and efficiency for omega-3 fatty acid protection.