The aim of present investigation was the preparation of dodecylamine template-based hexagonal mesoporous silica (HMS) as a carrier for poorly water-soluble drug (fenofibrate). HMS material has distinctive characteristics such as easy synthesis, high surface area and wormhole pores. These characteristics are highly admirable to make use of it as a carrier in drug delivery system. HMS was prepared by pH and temperature-independent process. Fenofibrate was loaded into the HMS by solvent immersion method using organic solvent. The BET surface area of HMS was evaluated by nitrogen adsorption/desorption analysis. HMS and drug-loaded HMS were characterized by differential scanning calorimetry (DSC), X-ray powder diffraction (XRPD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and contact angle study. The HMS-based system was also evaluated for in vitro and in vivo study as compared to plain drug. The BET surface area of HMS was found 974 m2/g with a narrow pore size average of 2.6 nm. The DSC and XRD study confirmed the amorphization of drug within the HMS. SEM and TEM study showed morphological features of HMS as well as revealed the wormhole porous structure. Contact angle study showed improvement in aqueous wetting property of drug within the HMS (contact angle 46°). The In vitro drug release study showed a remarkable dissolution enhancement in HMS-based system as compared to plain drug. In vivo pharmacodynamic study (hyperlipidaemia model) exhibited HMS-based formulation was significantly improved the bioavailability of fenofibrate. Thus, HMS has admirable properties; makes it a potential carrier for delivery system of poorly water-soluble drugs.