(1) Background: The growing prevalence of obesity, diabetes, hypertension, and declining physical fitness among children and adolescents due to sedentary lifestyles has increased attention toward preventive intervention to tackle this issue. This study investigated the age-related effects of high-intensity functional training (HIFT), based on bodyweight resistance exercises conducted during physical education lessons, on muscle mass and strength improvement. (2) Methods: Adolescent males (n = 116) were allocated to four HIFT experimental groups (EGs) and four standard physical education program control groups (CGs) according to age (15, 16, 17, and 18 years [y]). The changes in muscle mass (absolute and relative to height [SMI]), hand–grip strength (HGS), sit-ups (SUs), and standing broad jump (SBJ) were analyzed using two-way analysis of variance (ANOVA) with Bonferroni tests. (3) Results: HIFT significantly increased muscle mass and scores in all strength tests (p < 0.01), while chronological age was significant for HGS (p < 0.01). Interactions between HIFT and chronological age categories were observed for HGS (p = 0.01) and SBJ (p < 0.03). Detailed post hoc tests revealed improvement in muscle mass across all chronological age categories for both approaches (p < 0.05). The 18y-EG group improved HGS over their control peers (p < 0.01), the EG groups significantly improved their SU results (p < 0.01), and SBJ improved in the 15y-EG and 18y-EG groups compared to their control (p < 0.01). (4) Conclusions: This research highlights the effectiveness of a school-based HIFT program in promoting muscle mass gains and enhancing muscle strength among adolescents. The findings offer valuable insights for implementing bodyweight exercises during physical education classes.