Current physical activity and fitness levels among adolescents are low, increasing the risk of chronic disease. Although the efficacy of high intensity interval training (HIIT) for improving metabolic health is now well established, it is not known if this type of activity can be effective to improve adolescent health. The primary aim of this study is to assess the effectiveness and feasibility of embedding HIIT into the school day. A 3-arm pilot randomized controlled trial was conducted in one secondary school in Newcastle, Australia. Participants (n = 65; mean age = 15.8(0.6) years) were randomized into one of three conditions: aerobic exercise program (AEP) (n = 21), resistance and aerobic exercise program (RAP) (n = 22) and control (n = 22). The 8-week intervention consisted of three HIIT sessions per week (8-10 min/session), delivered during physical education (PE) lessons or at lunchtime. Assessments were conducted at baseline and post-intervention to detect changes in cardiorespiratory fitness (multi-stage shuttle-run), muscular fitness (push-up, standing long jump tests), body composition (Body Mass Index (BMI), BMI-z scores, waist circumference) and physical activity motivation (questionnaire), by researchers blinded to treatment allocation. Intervention effects for outcomes were examined using linear mixed models, and Cohen's d effect sizes were reported. Participants in the AEP and RAP groups had moderate intervention effects for waist circumference (p = 0.024), BMI-z (p = 0.037) and BMI (not significant) in comparison to the control group. A small intervention effect was also evident for cardiorespiratory fitness in the RAP group.