Cost of biodiesel can be reduced if produced from high free fatty acid non edible oils such as neem oil, jatropha etc. In the present study, two stage transesterification processes has been used to convert high free fatty acid neem oil into neem oil methyl ester. In this stage, experiments have conducted by varying methanol quantity (5, 10 and 15 % v / v of oil and reaction time (45 min, 60 min and 75 min) by keeping acid catalyst concentration (H2SO4, 1 % v / v) and reaction temperature (550C to 600C) constant. FFA level of neem oil has reduced to 0.8% by acid esterification at the optimized molar ratio of 3 (methanol quantity of 15 % v / v of oil) and reaction time (60 minutes). In the second stage, different concentration of methanol (20% to 45%, by vol), NaOH (0.3% to1.5%, by wt), reaction temperature (300C to 550C) and reaction time (60 min to 120 min) were selected in order to optimize the neem oil methyl ester yield. Maximum yield (85.50%) has obtained at optimum amount of methanol (35%), catalyst NaOH concentration (0.3%), temperature (550C) and reaction time (90 minutes).