In this study, we developed a two‐step enzymatic hydrolysis method followed by activated carbon adsorption to remove phenylalanine (Phe) from whey protein. The results showed that the free rate of Phe after sequential enzymatic hydrolysis of trypsin and flavorzyme was 90.8%. After adsorption by activated carbon No. 1, the removal efficiency of Phe from the hydrolysates reached 89.79% at 2.19 mg/g protein equivalent. Therefore, low Phe protein hydrolysates (LPHs) can be used to prepare low Phe food for phenylketonuria patients who cannot metabolise Phe properly by themselves and need to maintain a low Phe diet for life.