Purpose: The purpose of this study was to investigate the effect of HIIT training on body composition and fitness in female adolescents and compare with regular physical education classes. Method: A total participant sample consisted of 40 adolescent females from the secondary grammar school, who were randomly assigned to the experimental group (EG-16.44 ± 0.68 years) or the control group (CG-16.73 ± 0.62 years). The experimental group completed participation in a 12-week HIIT program, whereas the control group continued with their regular physical education classes. Testing of body composition and physical fitness was conducted in two stages: an initial test prior to the start of the experimental program, and a final measurement 12 weeks later. Results: The main findings indicate that both EG and CG significantly improved most body composition (body mass: p = 0.008, p = 0.013; BMI (EG only): p = 0.005; body fat: p = 0.013, p = 0.013, respectively) and physical fitness parameters (handgrip strength (right): p = 0.017, p = 0.032; standing long jump: p = 0.000, p = 0.000; sit and reach (EG only): p = 0.001; SJ (CG only): p = 0.008; 4 × 10 agility running test: p = 0.016, p = 0.004; sit ups for 30s. (CG only): p = 0.000; throwing a medicine ball from lying on back: p = 0.000, p = 0.036; shuttle run (VO2max): p = 0.000, p = 0.012; shuttle run (m): p = 0.000, p = 0.003, respectively). There was no significant interaction between group and time. Conclusion: Although both the HIIT and control groups demonstrated significant improvements, there were no significant differences between them. The findings suggest that HIIT training has the potential to be an effective method for improving physical fitness in school settings.