Recent evidences have shown catalyst structure sensitivity of electrocatalytic hydrogenation (ECH) of organic molecules in aqueous phase. In this study, ECH of glucose and xylose was investigated using gold nanoparticles (AuNPs) on activated carbon fiber (CF) support as catalyst. CF supported AuNPs catalysts (CF/AuNPs) were synthesized by deposition-precipitation method and were characterized by physicochemical (SEM, TEM, XRD, N2 physisorption, ICP-OES) and electrochemical methods. Chemical or thermal pre-treatment of CF prior to Au deposition resulted in different AuNPs size distributions. The activity towards glucose or xylose ECH were observed to be dependent on the particle size of AuNPs and the applied potential. Compared to a polycrystalline Au catalyst, higher reaction rates for glucose and xylose ECH were observed for a CF/AuNPs catalyst with a higher surface area. This indicates that the activity of Au towards glucose and xylose ECH is dependent on the surface area and particle size, and particle size control can be achieved by simple chemical or thermal pretreatment of the catalyst support.