The effect of the pore size of Pd/MCM-41 on the catalytic activity and selectivity in partial hydrogenation of canola-oil-derived biodiesel was studied under mild reaction conditions. The catalysts with different pore sizes were obtained by varying the amount of aqueous ammonia added during the synthesis: Pd/MCM-41-a8, Pd/MCM-41-aS, and Pd/MCM-41-a3 with average pore diameters of 3.72, 3.99, and 7.55 nm, respectively. The supports and supported Pd catalysts were characterized by Brunauer Emmett Teller surface area analysis, X-ray powder diffraction, transmission electron microscopy, CO pulse chemisorption, and temperature - programmed desorption of ammonia. The highest hydrogenation activity was found for the largest pore catalyst, Pd/MCM-41-a3, as presented in term of the turnover frequency (TOF), whereas Pd/MCM41-a8 and Pd/MCM-41-a5 provided higher selectivity toward cis-monounsaturated fatty acid methyl ester (FAME), which was attributed to their limited pore dimension. The correlation between the catalyst pore size and maximum diameter of major compounds (C18 FAMEs) was introduced and used to explain the results of TOF and selectivity.