Hydrodeoxygenation (HDO) of pyrolysis oil fractions was studied to better understand the HDO of whole pyrolysis oil and to assess the possibility to use individual upgrading routes for these fractions. By mixing pyrolysis oil and water in a 2:1 weight ratio, two fractions were obtained: an oil fraction (OFWA) containing 32 wt% of the organics from the whole oil and an aqueous fraction water addition (AFWA) with the remaining organics. These fractions (and also the whole pyrolysis oil as the reference) were treated under HDO conditions at different temperatures (220, 270 and 310 °C), a constant total pressure of 190 bar, and using 5 wt% Ru/C catalyst. An oil product phase was obtained from all the feedstocks; even from AFWA, 29 wt% oil yield was obtained. Quality parameters (such as coking tendency and H/C) for the resulting HDO oils differed considerably, with the quality of the oil from AFWA being the highest. These HDO oils were evaluated by co-processing with an excess of fossil feeds in catalytic cracking and hydrodesulfurisation (HDS) lab-scale units. All co-processing experiments were successfully conducted without operational problems. Despite the quality differences of the (pure) HDO oils, the product yields upon catalytic cracking of their blends with Long Residue were similar. During co-processing of HDO oils and straight run gas oil in a HDS unit, competition between HDS and HDO reactions was observed without permanent catalyst deactivation. The resulting molecular weight distribution of the co-processed HDO/fossil oil was similar to when hydrotreating only fossil oil and independent of the origin of the HDO oil.