A clean straightforward laser ablation method in deionized (DI) water is reported for the synthesis of Molybdenum (Mo) and Nickel (Ni) nanoparticles (NPs). The structural, morphological, and optical properties of the as-synthesized nanoparticles were investigated. Particle size was estimated to be less than 10 nm, the UV–vis spectra of the samples show the formation of H2MoO4 and NiO. The XRD results for the Ni sample show the presence of two phases, cubic nickel oxide, and an fcc metallic nickel phase, indicating the possible formation of Ni/NiO compound. The nanoparticles synthesized were used as precursors in the production of a NiMo/γ-Al2O3 catalyst. The textural and structural properties, chemical composition, and catalytic performance in a hydrodesulfurization (HDS) reaction are reported. The textural and structural properties results show the lack of pore-blocking due to the small sizes and the distribution of the metallic nanoparticles on the support. Chemical composition measured by XPS shows a ratio Ni/Mo of 1.34. Therefore, possibly Ni was deposited on Mo covering part of its active area, occupying active sites of Mo, removing its effective surface and resulting in a relatively low conversion of DBT (17%). A lower Ni/Mo ratio is required to improve the model system, which could be achieved by changing parameters at the production of the nanoparticles. The model system can also be further tuned by changing the size of the nanoparticles.