As adolescents spend the majority of their time focused on exams and assignments, they do not have sufficient time to engage in physical activity; this lack of physical activity is an important public health concern. This study aimed to investigate how school-based physical activity programs affect the health-related physical fitness of adolescents in the Republic of Korea. For this study, a total of 120 high school students participated in a school-based physical activity program that included badminton and table tennis for 15 weeks each (35 min/day, three times a week), with a total of 30 weeks for one academic year. The parameters for health-related physical fitness measured muscle strength (handgrip strength), power (standing long jump), cardiorespiratory fitness (shuttle run test), flexibility (sit and reach), body mass index (BMI), and the total score. The results revealed a statistically significant improvement in muscle strength (p < 0.001), power (p < 0.001), cardiorespiratory fitness (p < 0.001), flexibility (p = 0.005), and the overall health-related physical fitness score (p = 0.001). However, students' BMI showed no significant difference before and after participation (p = 0.825). The results of this study indicated that school-based physical activity programs can have a positive effect on the health-related physical fitness of adolescents.