This study aimed to develop a physical education fitness program for adolescents to counteract the declining physical activity levels caused by the COVID-19 pandemic, as well as to investigate the program’s effect. This mixed-methods study developed and implemented a five-component “Music Beeps” (MB) program to promote adolescents’ physical fitness. A total of 240 students from two high schools in South Korea—divided into experimental and control groups—participated in 32 sessions over 16 weeks. The changes in students’ fitness were analyzed, and the educational effects were examined via inductive analysis of the observation logs and group and in-depth interviews. The results demonstrated that, whereas the comparison group demonstrated no statistically significant changes in power, muscular strength and endurance, or cardiopulmonary endurance, the experimental group showed changes in all these variables, along with changes in flexibility. Further, the MB program had significant educational effects. First, students reported that musical cues enhanced their fitness motivation and sense of responsibility. Second, record-keeping and active participation contributed to self-led fitness management. Third, activity in a small space with few pieces of equipment led to the positive perception that the program was efficient and enabled regular exercise regardless of climate conditions.