The purpose of this study is to validate the application of GATE (Geant4 Application for Tomographic Emission) Monte Carlo simulation toolkit to model the performance characteristics of Siemens Inveon small animal PET system. GATE has been utilized to accurately create a complete PET imaging system model, including system geometry, physics process, signal processing and time-dependent effects. The GATE output data were histogrammed into 3D sinograms and subsequently processed by the Software of Tomography Reconstruction (STIR) to reconstruct 3D PET images. The simulation results were validated against experimental data in accordance with the NEMA NU-4 2008 protocol for standardized evaluation of spatial resolution, sensitivity, scatter fraction (SF) and noise equivalent counting rate (NECR) of a preclinical PET system. An agreement of less than 3% was obtained between the spatial resolution of the simulated and experimental results. The simulated peak NECR of mouse-size phantom agreed with the experimental result, while for the rat-size phantom simulated value was higher than experimental result. The simulated and experimental SFs of mouse- and rat- size phantom both reach an agreement of less than 2%. Therefore, it has been shown the feasibility of our GATE model to accurately simulate, within certain limits, all major performance characteristics of Inveon PET system. In future, the validated model can be utilized to validate, assess and further develop reconstruction algorithms and PET acquisition protocols.