Molecular distillation is industrially useful in the purification of highly oxidative oils and fats, and their derivatives. Free Fatty Acids (FFAs) were isolated from high free fatty acid crude palm oil (HFFA-CPO) using molecular distillation. The isolation conditions were set-up with feeder flow rate of 2.3 g/min, wipers speed of 350 rpm, evaporator temperature ranging from 150 °C to 265 °C and pressure at 10 torr respectively. The results showed that the yield of crude palm oil after separation (CPOAS) was 88 % (wt/wt). The physicochemical properties of CPOAS showed a distinct difference in acid value, FFA content, iodine value and hydroxyl value compared to that of HFFA-CPO and it is more favourable for food product usage. The results showed that CPOAS has lower acid value (reduced from 21.3 ± 0.1 to 2.1 ± 0.01 mg NaOH/g), increased iodine value from 50.6 ± 0.2 to 53.5 ± 0.2 mg KOH/g, reduced hydroxyl value from 43.4 ± 0.2 to 25.5 ± 0.1 mg KOH/g and lower FFA content from 9.4 ± 0.1 % to 0.9 ± 0.1 % in CPOAS respectively. The work has proven that molecular distillation is an effective method for the separation of FFA from high free fatty acid crude palm oil.