In this paper, a complete three-dimensional (3D) RF model of the cyclotron coaxial resonator—including the coaxial sliding shorts, the “Liner” vacuum chamber, the coupler, the trimmer, and the high RF voltage “Dee” structures—has been developed. An eigenmode analysis was used to simulate the tuning of the resonator in the operating frequency range of 15–48 MHz obtained by two movable sliding shorts and a trimmer. A driven analysis has been performed in order to compute the |S11| parameter (or impedance matching) of the cavity excited by a movable coaxial power coupler. The numerical simulations have been performed using the different peculiarities of two commercial tools, COMSOL Multiphysics and CST microwave studio. Experimental validation of the developed model is presented. The evidence of an unwanted electric field component, orthogonal to the accelerating field, was discovered and a mitigation is also proposed. The impact of the proposed modification was evaluated by using a 3D beam dynamics code under development in the framework of the Superconducting Cyclotron upgrade ongoing at INFN-LNS.