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Despite well-established benefits, the majority of young people around the globe are not sufficiently active. In many countries, including Australia, physical activity (i.e. physical education and school sport) is not mandatory in the final two years of high school (i.e. senior school years). The aim of this study was to assess the impact of a time-efficient physical activity intervention on senior school students' on-task behaviour and subjective vitality. This was a sub-study of the Burn 2 Learn (B2L) cluster randomised controlled trial, which included two cohorts. Participants for this sub-study (N = 221) were from 10 secondary schools (23 classes) located in New South Wales, Australia (Cohort 2). Teachers allocated to the B2L intervention group were provided with training, resources and support to facilitate the delivery of two high-intensity activity breaks per week during lesson time for five weeks. A wait-list control was used as comparison group. On-task behaviour was assessed at baseline and post-test, using a momentary time sampling procedure and expressed as a percentage of lesson time. At post-test, subjective vitality was assessed at the start and end of the lesson using a validated questionnaire. Significant group-by-time effects were observed for students' on-task behaviour in favour of the B2L group [adjusted mean difference = 19.3% of lesson time (95% CI, 0.8 to 37.8), p = 0.042, d = 0.43]. At post-test, significant group-by-time effects were observed for students' subjective vitality favouring the B2L group [adjusted mean difference = 0.67 units (95% CI, 0.3 to 1.0), p < 0.001, d = 0.36]. The B2L intervention was successful in improving senior school students' on-task behaviour and their subjective vitality. These findings highlight the potential academic benefits of re-allocating curriculum time to physical activity during the senior school years.