The use of mesostructurated materials as cobalt support for the Fischer–Tropsch Synthesis (FTS) has taken increasing importance in the last decade. However, little use has been made of the hexagonal mesoporous silica (HMS), as most of the work has been reported for Co/MCM-41 and Co/SBA-15 catalytic systems. The effect of cobalt loading, impregnation method, particle size and pretreatment, on the catalytic properties of cobalt supported on HMS catalysts for the Fischer–Tropsch Synthesis have been studied. Catalysts were synthesized by incipient wetness impregnation, using an aqueous solution of hexahydrated cobalt nitrate as precursor salt. Additionally, a series of catalysts was prepared using an ethylene diamine cobalt complex which enabled cobalt nanoparticles formation. All catalysts were characterized by X-ray diffraction (XRD), temperature programmed reduction (TPR), chemical analysis and nitrogen adsorption. Calcination pretreatment has great influence in the catalytic behavior of the cobalt catalysts. All the catalysts prepared showed high C5 + fraction selectivity, specifically towards the diesel fraction. The use of HMS as cobalt catalyst support for the Fischer–Tropsch Synthesis seems to be very promising. When SiO2 is used as support, C5 + hydrocarbons distribution shows a marked tendency towards C19 + fraction, while when HMS is used, the diesel fraction is favored. This result leads to the conclusion that the HMS pore structure produced a chain growth hindrance, tailoring the product distribution towards the diesel fraction.