Biodiesel has been considered as a reasonable replacement fuel for petroleum diesel. It has many advantages over petroleum diesel including its biodegradability and non-toxicity. In addition, it provides free aromatics and sulphur combustion and it is a greener fuel with lower carbon monoxide and hydrocarbons emissions. However, biodiesel has lower heating value and it is relatively more expensive than petroleum diesel. In an attempt to reduce the cost of biodiesel, waste cooking oil (WCO) has been considered as a competitive feedstock. It also provides more sustainability for the produced biodiesel as it is a result of transformation of waste to greener source of energy. The main concern for using WCO as a feedstock for biodiesel production is the presence of high concentration of free fatty acids (FFA), which result in saponification reaction while using the conventional alkaline catalysed process. Saponification lowers the biodiesel yield by preventing the separation of biodiesel from the product. In this study, a non-catalytic method for biodiesel production from WCO using supercritical methanol has been investigated. Two different feedstocks with different FFA concentration have been examined. Response surface methodology (RSM) using Box Behnken Design (BBD) and Central Composite Design (CCD) has been employed to analyse the effect of different reaction variables including methanol to oil (M:O) molar ratio, temperature, pressure and time on biodiesel yield. Numerical optimisation has been applied to determine the optimum conditions for maximum production of biodiesel for each feedstock. It has been concluded that the feedstock with higher FFA concentration produce higher biodiesel yield within the same reaction conditions. This result indicates the significance of using supercritical methanol technique for feedstocks with high FFA concentration as it enhances both esterification of FFA and transesterification of triglycerides (TG) to fatty acids methyl esters (FAME).