This article aims to understand the motion of the charged particles trapped in the Earth’s inner magnetosphere. The emphasis is on identifying the numerical scheme, which is appropriate to characterize the trajectories of the charged particles of different energies that enter the Earth’s magnetosphere and get trap along the magnetic field lines. These particles perform three different periodic motions, namely: gyration, bounce, and azimuthal drift. However, often, the gyration of the particle is ignored, and only the guiding center of the particle is traced to reduce the computational time. It is because the simulation of all three motions (gyro, bounce, and drift) together needed a robust numerical scheme, which has less numerical dissipation. We have developed a three-dimensional test particle simulation model in which the relativistic equation of motion is solved numerically using the fourth and sixth-order Runge-Kutta methods. The stability of the simulation model is verified by checking the conservation of total kinetic energy and adiabatic invariants linked with each type of motion. We found that the sixth-order Runge-Kutta method is suitable to trace the complete trajectories of both proton and electron of a wide energy range, 5 keV to 250 MeV for L = 2–6. We have estimated the bounce and drift periods from the simulations, and they are found to be in good agreement with the theory. The study implies that a simulation model with sixth-order Runge-Kutta method can be applied to the time-vary, non-analytical form of magnetic configuration in future studies to understand the dynamics of charged particles trapped in Earth’s magnetosphere.