Pseudo-random number generators are the heart of Monte Carlo simulations. Generally, the quality of random number generators may affect the output of the simulation. Any GEANT4-based Monte Carlo tool has different random number generators. The GATE toolkit, a widely used package in nuclear medicine, also provides three generators for the users to select. In this study, we used the random number generators in identical simulations in order to check their possible effect on the outputs of simulations. Simulations were performed considering two point radiation sources, including electrons and photons at the center of water phantoms, for eight monoenergies between 10 and 1000 keV. Paired t-test, normal probability plot and Bland–Altman plots were used to compare pairs of corresponding results. In all the simulations, the average values of data derived using different random number generators were almost the same with small differences. However, statistical variation was considerably high, particularly in the estimation of track length of electrons and the spectra of X-ray radiation due to the interaction of electron with atoms. At high energies noticeable differences were observed in simulation runtimes using different generators. There is no systematic difference between average parameters derived using different random number generators. Statistical fluctuations in corresponding data derived using random number generators are considerably high. It is recommended to use a large number of histories in simulation if the individual points in a series of data points are important. Due to simulation runtimes considerations, selection of Mersenne Twister generator is advocated.