The present work aims to find out the influence of flow pattern on pressure drop and fatty acid methyl ester (FAME) yield in a reactive system. Experiments are carried out with Jatropha oil and methanol by using potassium hydroxide (KOH) as catalyst for biodiesel production in two serpentine minireactors made of glass capillary of 2-mm internal diameter. One is having a circular cross section, and the other is annulus. Slug flow, slug with droplet flow, and dispersed flow are observed in both the reactors. Effects of flow distribution on pressure drop and FAME yield have been studied. FAME yield of 98.5% is observed in both reactors for a molar ratio 20 (methanol to Jatropha oil), and the time for this yield in the first reactor is 16.6 minutes and that for the second reactor is 7.7 minutes. Higher yield also resulted in lower pressure drop due to lower viscosity of biodiesel in comparison with oil.