The quality of commercial fish oil products can be difficult to maintain because of the rapid lipid oxidation attributable to the high number of polyunsaturated fatty acids (PUFA), specifically eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). While it is known that oxidation in fish oil is generally the result of a direct interaction with oxygen and fatty acid radicals, there are very few studies that investigate the oxidation kinetics of fish oil supplements. This study uses hydroperoxides, a primary oxidation product, to model the oxidation kinetics of two commercially available fish oil supplements with different EPA and DHA contents. Pseudo first order kinetics were assumed, and rate constants were determined for temperatures between 4 and 60 °C. This data was fit to the Arrhenius model, and activation energies (E(a)) were determined for each sample. Both E(a) agreed with values found in the literature, with the lower PUFA sample having a lower E(a). The oil with a lower PUFA content fit the first-order kinetics model at temperatures ≥20 °C and ≤40 °C, while the higher PUFA oil demonstrated first-order kinetics at temperatures ≥4 °C and ≤40 °C. When the temperature was raised to 60 °C, the model no longer applied. This indicates that accelerated testing of fish oil should be conducted at temperatures ≤40 °C.