Six quaternary phosphonium salts (QPSs) in combination with phosphotungstic heteropolyacid, H3PW12O40, were tested in the epoxidation of rapeseed oil fatty acid methyl esters with a hydrogen peroxide aqueous solution. The QPSs consisted of trihexyl(tetradecyl)phosphonium [P6], tributyl-tetradecylphosphonium [P4] or tetraoctylphosphonium [P8] cation and different anions—chloride (Cl−), bromide (Br−), tetrafluoroborate (BF4−), bis(trifluoromethylsulfonyl)amide (NTf2−), bis(2,4,4-trimethyl-pentyl)phosphinate (Phosf−). The influence of the kind of QPS and temperature on the epoxy number, iodine number, glycol content has been determined. The epoxidation was confirmed using Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR) and elemental analysis CHO. Two QPSs with a trihexyltetradecyphosphonium cation—[P6][Fosf] and [P6][Cl]—were selected as the most effective in the studied epoxidation process. The proposed kinetic model takes into consideration the two reactions, namely, epoxidation and epoxy ring opening involving the formation of hydroxyl groups. The rate constants and activation energies for epoxidation fatty acid methyl esters were determined.