This study was to investigate the effect of high intensity interval training on health related fitness and bone mineral density in middle school girls. For this purpose, the participants randomly selected 24 girls in the second grade at Middle School, assigned 12 randomly to the exercise and control group each, and measured their health related fitness and bone mineral density before and after the experiment. Two-way repeated ANOVA was used to analyze within and between group differences. There were significant differences in muscle strength, flexibility according to time and that interactions happened between group and time in muscle strength, cardiopulmonary endurance, flexibility, and % body fat. No significant differences were found in bone mineral density according to group, time, and group×time interaction. It is thought that high intensity interval training can be effectively used to promote health and improve physical fitness regardless of time and place for adolescents who cannot participate in training due to lack of time.