Waste edible oils are an alternative source of high‐value natural compounds. Vitamin E can be recovered from palm oil refining residues by molecular distillation. However, the presence of other lipophilic molecules compromises the selective separation of vitamin E. Esterification of the free fatty acids can enhance the selective separation of vitamin E by molecular distillation, but the conditions for carrying out the reaction need to be investigated to simultaneously ensure the conversion of free fatty acids and the reduction of vitamin E losses. Thus, this study investigated the effect of the esterification of the industrial waste on the recovery of vitamin E by molecular distillation. Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and analysis for fats and oils preconized by the American Oil Chemists' Society (AOCS) were used in the characterization of the industrial waste. Determination of the best condition to carry out the reaction was obtained by a central composite rotational design (CCRD) using the response surface methodology (RSM) and the desirability profile. The results showed that the best condition for the esterification was at 64°C, 213 min, 2 wt.% sulphuric acid, and a 10/1 methanol/free fatty acids molar ratio. This reaction condition achieved 97.9% conversion of free fatty acids and less than 3% of vitamin E loss. The esterification promoted concentration of vitamin E in the residue stream (145.4%) and reduction in the distillate stream (87.8%). Therefore, the obtained results presented a suitable route to obtaining vitamin E concentrate and adding value to an industrial residue.