The experimental parameters for biodiesel production from para rubber seed oil and methanol using a SO3H-MCM-41 catalyst were optimized statistically. The SO3H-MCM-41 catalyst was synthesized by co-condensation in the presence of tetraethyl orthosilicate, 3-mercaptopropyl (methyl) dimethoxysilane (MPMDS) and cetyl-trimethylammonium bromide. In the last step, the solid catalyst (SH-MCM41) was oxidized by H2O2 to SO3H-MCM-41. The acid capacity of the obtained SO3H-MCM-41 catalyst was quantified by back titration with 0.1 M sodium hydroxide. The physical and chemical properties of the SO3H-MCM-41 were characterized by nitrogen adsorption/desorption, X-ray diffractometry, Fourier transform infrared spectroscopy and thermogravimetric analysis. The effect of varying the catalyst loading (wt.%), reaction time (h) and temperature (°C) and molar composition of MPMDS on the biodiesel yield were investigated using a 2k factorial design. The optimal conditions to maximize the biodiesel yield, obtained from the response surface analysis using a Box–Behnken design, was a 14.5 wt.% catalyst loading, and a reaction time and temperature of 48 h and 129.6 °C. Under these conditions a fatty acid methyl ester (biodiesel) yield of 84% was predicted, and an 83.10 ± 0.39% yield experimentally obtained.