A novel analytical method was developed for quantifying total mercury in fuel oils using methionine as a capping reagent. Methionine was added to fuel and standard solutions as a preserving agent before microwave-assisted hydrogen peroxide digestion (MW-AHPD). To the best of our knowledge, it is the first-time methionine was used as a capping reagent for the total determination of mercury in fuel oils using ICP-OES with a pneumatic nebulizer. Multivariate optimization tools (two-level half factorial and central composite design) were used to investigate the most influential parameters of the MW-AHPD method. The best conditions were 0.1 g sample mass, 5 mol L−1 [H2O2], 5. 95 mol L−1 [methionine], 36 min and 200 °C with accepted trueness (93–107%) and precision (1.94%). The developed MW-AHPD procedure provided a coefficient of determination (R2) of 0.9989, limit of detection (LOD) of 0.25 µg L−1 and limit of quantification (LOQ) of 0.8 µg L−1. The newly developed MW-AHPD procedure was validated using hydride generation-ICP-OES and there was no statistical difference at 95% confidence level between the newly developed method and the standard protocol. Therefore, the newly developed MW-AHPD procedure was applied with coal, crude oil, gasoline, diesel oil, and kerosine samples and the concentration levels were from 0.876 ± 0.023 to 0.938 ± 0.082 µgg−1, 0.383 ± 0.043 to 0.506 ± 105 µgg−1, 0.306 ± 0.010 to 0.390 ± 0035 µgg−1, 0.360 ± 0.003 to 0.431 ± 0.001 µgg−1 and < DL, respectively.