This thesis examines the various aspects of catalytically deoxygenating biomass-derived feedstocks including the relevant catalyst materials, conditions and equipment. Preliminary investigations probed the ability of T316 SS, as a reactor material, to perform as an effective hydrogenation catalyst at temperatures above 100 oC, under reducing aqueous-acidic media. Additionally, an external apparatus was developed in order to facilitate the optimization of catalytic hydrogenations. The accuracy and applicability of this system was confirmed using the reduction of levulinic acid to γ-valerolactone. Accurate information pertaining to the quantity of hydrogen consumed was obtained in addition to in situ differential rates reaction allowing for the derivation of the integrated rate law. Subsequently, the newly designed uptake system was used to monitor, and effectively optimize, the deoxygenation of a series of complex furfural-derived substrates towards the attempted production of high-energy density fuels. Commercially available Pd/C and Ru/C catalysts were employed, unsuccessfully, under a variety of reaction conditions.