Purpose: The purpose of this study was to investigate the effects of complex training on injury, flexibility, and muscle stiffness in high school male football players. Methods: A total of 60 football players were included in the study and were divided into three groups viz. the complex training group (CTG), 11+ training group (11 + TG), and traditional training group (TTG). Injuries were recorded based on the prospective investigation method after starting the study, and the flexibility and muscle stiffness of the subjects were evaluated. Results: The research results showed that the injury rate per match was significantly lower in the CTG and 11 + TG than the TTG. In the CTG, the flexibility of the hamstrings significantly increased and the stiffness of the rectus femoris (RF), biceps femoris (BF), and tensor fascia latae (TFL) muscles significantly decreased (p < 0.05). In the 11 + TG, the stiffness of the RF significantly decreased (p < 0.05). In the TTG, the flexibility of the hamstrings significantly increased (p < 0.05). Hamstring flexibility showed a significantly higher increase in the CTG and TTG compared to the 11 + TG (p < 0.05). Also, the stiffness of the RF and TFL muscles showed a significantly higher decrease in the CTG compared to the 11 + TG and TTG (p < 0.05). The stiffness of the BF muscles too showed a more significant decrease in the CTG compared to the TTG (p < 0.05). Conclusion The complex training method of the Fédération International de Football Association (FIFA) 11+ and self-myofascial release (SMFR) as a warm-up program, prevent injuries, enhance flexibility, and lower muscle stiffness of football players in high school. Thus, it is necessary to ensure the widespread use of the complex training program by instructors and players under the supervision of the Korea Football Association (KFA), given its reliability in preventing injuries and improving the performance of football players.