In this study, a simple and robust derivatisation-free method has been developed using a gas chromatograph (GC), which has been validated as a suitable analysis for free fatty acids (FFAs) of waste cooking oil (WCO). As biodiesel synthesis from high acid value WCO involves pre-treatment steps, a non-catalytic approach has been employed for biodiesel production. This work has focused on the esterification of FFAs of high acidity feedstock for fatty acid methyl esters (FAME) production. The effect of four independent controllable factors, i.e. methanol to oil (M:O) molar ratio, temperature, pressure and time on FFAs conversion has been investigated. Response Surface Methodology (RSM) via Central Composite Design (CCD) has been implemented for designing experimental runs and optimising the process variables for maximum FFAs conversion. Four quadratic regression models have been developed representing an empirical relationship between reaction variables and responses. The adequacy of the predicted models has been checked by numerous statistical validation techniques including analysis of variance (ANOVA) at 95% confidence level. The developed optimum conditions have been reported at 25:1, 256 °C, 110 bar and 16.6 min for M:O molar ratio, temperature, pressure and time, respectively. The predicted optimal conditions have been validated experimentally with 0.22% relative error.