Background: Kickboxing is a combat sport that is complex in technique, tactics, and movement structure, and requires an adequate level of motor skills as a foundation for activities during competitions. General physical fitness, defined as the effect of the externalization of motor skills, is the basis for athletic training regardless of the sport. The aim of this study was to determine the effect of modified training based on the principles of CrossFit on the development of general physical fitness in a group of kickboxers compared to a control group. Methods: The study was experimental in nature and was conducted in a group of 60 kickboxers, divided into experimental and control groups. Participants were selected by purposive sampling, and the criteria were training experience, sports skill level (minimum class 1 athletes), and consent to participate in the experiment. The intervention in the study group involved the introduction of CrossFit-based training into a conventional kickboxing training program. General and special physical fitness of the athletes were diagnosed. Results: Statistically significant differences were found in general fitness in terms of abdominal strength (p < 0.001), pull-ups (p < 0.001), dynamometric measurement of handgrip force (p < 0.001) (kg), clap push-ups (p < 0.001), standing long jump (p < 0.001), shuttle run (p < 0.001), sit-and-reach (p < 0.001), and tapping (p < 0.001). Furthermore, changes in special fitness were also demonstrated for the special kickboxing fitness test (SKFT) (p < 0.02), the total number of punches (p < 0.001), punching speed (p < 0.001), and hip turning speed (p < 0.001). There was also a correlation between characteristics of general fitness and special fitness (p < 0.001). Conclusions: The experimental training program based on the principles of CrossFit training had a positive effect on the general and special kickboxing physical fitness.