Abstract The global demand for sustainable and ecologically friendly energy sources has spurred biodiesel research. Civilization, urbanization, and population growth have drastically boosted transportation energy consumption. Energy demand is causing fossil fuel crises. Replace petroleum diesel to solve energy and environmental problems. Biofuels have very vast scope in the area of energy sector. Karanja oil, derived from the seeds of the Karanja tree (Pongamia pinnata), is a promising biodiesel feedstock due to its high Free Fatty Acid content. This study uses Oscillatory Baffled Reactor (OBR) to produce biodiesel from Karanja oil. The feedstock is high-FFA Karanja oil trans-esterified in two steps. In OBR, reaction time is only 15 min, whereas in conventional reactor it takes 1–2 h to produce biodiesel. Optimizing biodiesel synthesis involved varying H2SO4 concentrations from 1 vol% to 5 vol% and 0.3 to1.0 wt% of NaOH concentration for first and second step respectively. Oil-to-alcohol molar ratios 1:6, 1:9 and 1:12. Optimization occurs at 1:12 oil-to-alcohol ratio, 1 vol% H2SO4 catalyst, and 0.6 wt% NaOH catalyst. Studies have also examined how catalyst concentration and oil: alcohol molar ratio affect biodiesel conversion and physical qualities such kinetic viscosity, specific gravity, and acid value. This study shows that OBR can increase biodiesel production from high-FFA Karanja oil, which further opens up opportunities for additional study and improvement.