The impact of the addition of commercial thyme (TEO) and rosemary essential oil (REO) and butylated hydroxytoluene (BHT, 0.01%) combined with sunflower oil on the lipid quality of Atlantic bonito was investigated during shallow frying. Atlantic bonito treated with TEO and REO had significantly lower lipid content than control and BHT-treated samples (p < 0.05). As compared to controls, the addition of both synthetic and natural antioxidants to sunflower oil resulted in a significant decrease in the peroxide values (PV), free fatty acids (FFA), and thiobarbituric acid reactive substances (TBARs) values of samples. These decreases had a similar effect in both essential oils (EOs) groups, inversely proportional to the increased used concentration. The addition of all EOs into the sunflower oil, except for 0.9% REO group, significantly increased the amount of total saturated fatty acid (∑SFA). Although the addition of EOs at different concentrations has a significant effect on the total monounsaturated fatty acids (∑MUFA) of fried Atlantic bonito, the highest MUFAs content was observed in the 0.6% thyme EO group. Our results indicated that the use of commercial TEO and REO seems to be effective in the protection of the amount of fatty acid compositions of Atlantic bonito, especially eicosapentaenoic (EPA) and docosahexaenoic acids (DHA). As a result, the lipid quality of Atlantic bonito during shallow frying was improved by all EOs used for the current study.