Hybrid silica-based porous aerogels containing propylsulfonic acid and methyl functionalities were prepared by co-condensation route from the corresponding mercaptopropyltriethoxysilane and methyltriethoxysilane precursors using aqueous ammonia as hydrolyzing agent in the absence of any organic templates. The hybrid aerogel was dried under supercritical CO2 and characterized by SEM, TEM, 13C CP-MAS NMR, 29Si MAS NMR, TG/DTA, and nitrogen adsorption/desorption analyses. The hybrid-silica aerogel containing propylsulfonic acid serves as an efficient heterogeneous acid catalyst in transesterification of fatty acid esters with methanol in a batch reactor.