To standardize the production process of ethyl ester from Pongamia oil, which has high free fatty acids, a two-stage transesterification was developed. In first-stage acid transesterification, parameters like ethanol, quantity, and reaction time were optimized to reduce free fatty acids below 1% using H2SO4 catalyst. In second-stage alkaline transesterification, parameters like molar ratio, degree proof of ethanol, catalyst concentration, and reaction temperature were optimized to obtain the highest yield with lower viscosity from pretreated oil. The ester recovery was estimated with spectrophotometry and was found to be 91%. The fuel characteristic properties of Pongamia ethyl ester were inline with specified BIS standards.