Pre-participation screening (PPS) in professional junior football is common practice. However, football players (FP) from non-professional football clubs may also be exposed to health risks, both internal and musculoskeletal. Therefore, the Bavarian Football Association (BFV) implemented a cardiological and orthopedic screening program for semi-professional FP in 2014. The purpose of this study was to obtain and present epidemiological data of pre-adolescent and adolescent semi-professional FP, including cardiac pathologies, past injuries, and orthopedic disorders. This study represents a retrospective analysis of semi-professional FP aged 11 to 14 years participating in the PPS program from 2014 to 2018, including their medical history, cardiac risk profiles, and the results of undergoing orthopedic and sports cardiology examinations. Overall, 362 male and 162 female FP could be included. More than 20% of the FP indicated suffering from one or more medical conditions. Cardiac abnormalities were reported in 30 (5.7%) FP. Further cardiological diagnostics were recommended for 3% of the FP due to findings while undergoing the PPS. Orthopedic disorders could be detected in 51 (9.7%) FP. Of the reported injuries, 44.3% could be categorized as overuse injuries. In order to guarantee extensive preventive sports medical care for semi-professional junior FP, a PPS concept should include a basic orthopedic examination in addition to cardiological screening due to a high rate of overuse injuries and cardiac abnormalities among pre-adolescent and adolescent FP. Further studies are needed in junior football to gain epidemiological data on injury occurrence and cardiac abnormalities on an amateur level to evaluate possible PPS programs, even on an amateur level.