In this study, the preparation of nickel and cobalt incorporated MCM-41 (metal-MCM-41) with Si/Al = 10, Si/Mo = 10 and Si/Co and Si/Ni as 50 was done. Then molybdenum was impregnated on Ni-MCM-41 and Co-MCM-41 by incipient wetness impregnation method. MCM-41 based catalysts were characterized by XRD, surface area, pore volume, pore-size distribution, and temperature programmed reduction (TPR). The catalysts were evaluated for hydrodesulfurization of model compounds thiophene and benzothiophene in pulse reactor at atmospheric pressure and at different temperatures. HDS of dibenzothiophene dissolved in dodecane, was also performed in a batch autoclave reactor at high pressure and temperature. The results of hydrodesulfurization activity indicate that when impregnated with molybdenum the prepared metal-MCM-41 showed higher activity as compared to commercial catalyst. Mo-CoMCM-41 showed highest conversion per mole of metal in hydrodesulfurization of thiophene and benzothiophene. For comparison purposes, a sample of NiMo-Y zeolite catalyst was also prepared and evaluated