High-Intensity Interval Training (HIIT) promises high training effects on aerobic fitness in children, adolescents and adults in a relatively short time. It is therefore well-established in professional training settings. HIIT methods could also be suited to Physical Education (P.E.) lessons and contribute to students’ health and fitness. Since HIIT sessions need little time and equipment, they can be efficiently implemented in P.E. However, there are few studies which have examined non-running-based HIIT programs in the school sport setting. We therefore conducted an intervention study including 121 students aged 11–15 attending a secondary school in Baden Württemberg, Germany. The effects of three different forms of HIIT training varying in duration and content (4 × 4 HIIT, 12 × 1 HIIT, CIRCUIT) were analyzed. The training was conducted twice a week over 6 weeks (10–12 sessions). Strength and endurance performances were determined in pre- and posttests prior to and after the intervention. Results verified that all three HIIT programs led to significant improvements in aerobic fitness (p < 0.001; part ŋ2 = 0.549) with no significant interaction between time x group. In contrast to the running-based HIIT sessions, CIRCUIT training also led to significant improvements in all of the measured strength parameters. Retrospectively, students were asked to assess their perception of the training intervention. The HIIT sessions were well-suited to students who considered themselves as “athletic”. Less athletic students found it difficult to reach the necessary intensity levels. The evaluation showed that endurance training conducted in P.E. lessons needs a variety of different contents in order to sufficiently motivate students. Students perceiving themselves as “unathletic” may need additional support to reach the required intensities of HIIT. Circuit training sessions using whole-body drills can be efficiently implemented in the P.E. setting and contribute to students’ health and fitness.