Monte Carlo simulation is widely used in emission tomography, in order to assess image reconstruction algorithms and correction techniques, for system optimization, and study the parameters affecting the system performance. In the current study, the performance of the IRI-microPET system was simulated using the GATE Monte Carlo code and a number of performance parameters, including spatial resolution, scatter fraction, sensitivity, RMS contrast, and signal-to-noise ratio, evaluated and compared to the corresponding measured values. The results showed an excellent agreement between simulated and measured data: The experimental and simulated spatial resolutions (radial) for 18F in the center of the AFOV were 1.81 mm and 1.65 mm, respectively. The difference between the experimental and simulated sensitivities of the system was <7%. Simulated and experimental scatter fractions differed less than 9% for the mouse phantom in different timing windows. The validation study of the image quality indicated a good agreement in RMS contrast and signal-to-noise ratio. Also, system performance was compared with the two available commercial scanners which were simulated using GATE code. In conclusion, the assessment of the Monte Carlo modeling of the IRI-microPET system reveals that the GATE code is a flexible and accurate tool for describing the response of an animal PET system.