Integration of renewable resources into transportation fuel system requires investigation of resource compatibility with existing infrastructure and exploitation of potential integration points within transportation fuel system. This work focuses on co-processing fast pyrolysis oil (FPO) in refinery FCC units. In this work, a novel methodology is proposed for the modelling of catalytic cracking of a blend of vacuum gas oil (VGO) and fast pyrolysis oil in an advanced cracking evaluation (ACE-R) FCC unit. A new molecular-level characterisation method, based on MTHS matrix approach, is developed for the characterisation of blended feedstock. Molecular-level reaction models are then constructed based on large scale and complex reaction networks synthesised using MTHS matrix framework. The total number of reactions used to synthesise the reaction network in this work is 328. Kinetic parameters tuning problem is formulated as an optimisation problem in which the objective function is to minimise the difference between measured and predicted products yields at various conversion levels. An overall good agreement between measured and predicted yields is obtained using the developed kinetic model for VGO: FPO blending ratio, C/O ratio and reaction temperature of 95:5, 5 and 530 degrees C, respectively. PONA composition in each layer of product stream (e.g. gasoline, diesel, gasoil, etc.), as well as oxygen compounds compositions and oxygen content is predicted. This creates potentials for rigorous optimisation of process parameters for refinery profit maximisation or better products' quality control. The methodology developed in this work can easily be extended to model other refinery processes.