Background: Low-volume high-intensity interval training holds promise for cardiometabolic health promotion in adolescents, but sustainable interventions must be practical and engaging. We examined the effect of a school-based multi-activity low-volume high-intensity interval training intervention on adolescents' cardiometabolic health. Methods: In an exploratory controlled before-and-after design, 101 adolescents (mean age ± standard deviation [SD] 14.0 ± 0.3 years) were recruited from four schools; two were designated as intervention sites (n = 41), and two as control (n = 60). The intervention comprised 4 to 7 repetitions of 45 s maximal effort exercise (basketball, boxing, dance and soccer drills) interspersed with 90-s rest, thrice weekly for 10 weeks. Outcomes were non-fasting blood lipids and glucose, waist circumference, high sensitivity C-reactive protein, resting blood pressure, physical activity, twenty-metre shuttle-run test performance and carotid artery intima-media thickness. The difference in the change from baseline (intervention minus control) was estimated for each outcome. Using magnitude-based inferences, we calculated the probability that the true population effect was beneficial, trivial, and harmful against a threshold for the minimum clinically important difference of 0.2 between-subject SDs. Results and Discussion: Mean (± SD) attendance for the intervention (expressed as percentage of available intervention sessions [n = 30]) was 77 ± 13%. Post-intervention, there were likely beneficial effects for triglycerides (-26%; 90% confidence interval -46% to 0%), waist circumference (-3.9 cm; -6.1 cm to -1.6 cm) and moderate-to-vigorous physical activity (+16 min; -5 to 38 min), and a possibly beneficial effect for twenty-metre shuttle-run test performance (+5 shuttles; -1 to 11 shuttles) in intervention participants (vs controls). The role of elevated triglycerides and waist circumference in cardiovascular disease and metabolic syndrome development underlines the importance of our findings. We also demonstrated that school-based low-volume high-intensity interval training can be delivered as intended, thus representing a novel and scalable means of improving aspects of adolescents' cardiometabolic health. Trial Registration: ClinicalTrials.gov NCT02626767.