Wireless charging devices for implantable cardiac pacemakers have not been clinically applied. For actual applications, safety assessments of a wireless charging system must be conducted. For systems with a certain power, frequency is one of the important factors that directly affect safety. This paper aims to study the safety evaluation method and optimal operation frequency of a cardiac pacemaker wireless charging system. The wireless power transfer (WPT) model considering the coils' AC resistance is established, which is more in line with the actual situation. The analytical solution to the current in coupling coils is derived, which reveals the effect of the frequency. The currents used in electromagnetic and thermal simulations are calculated or measured for different charging prototypes. A safety evaluation method that comprehensively considers specific absorption rate (SAR), electric field, efficiency, temperature rise and electromagnetic interference (EMI) is proposed. In particular, the temperature rise is an innovative perspective as it has rarely been studied in previous literatures. The optimal frequency of a 3 W wireless charging system for cardiac pacemaker is determined based on the results of safety evaluation. The theoretical temperature rise reaches the minimum at 203 kHz, and the theoretical energy loss reaches the minimum at 260 kHz. The comfort and safe frequency band is approximately from 150 kHz to 370 kHz based on theoretical and experimental results, and the optimal frequency band from 200 kHz to 300 kHz is recommended.