Background: The majority of children internationally are not sufficiently active. Integrating physical activity into academic lesson time may not only help increase children’s activity levels but also improve learning. The aim of this study was to assess the impact of a classroom-based physical activity intervention on primary school students’ physical activity levels and academic outcomes (i.e., on-task behavior, literacy and executive function skills). Methods: This cluster randomized controlled trial included students ( N = 283) from nine primary schools located in New South Wales, Australia. Schools were allocated to a control (n = 5 schools) or Thinking while Moving in English (TWM-E) (n = 4 schools) conditions. Teachers received professional learning (i.e. one day workshop), resources (e.g. drill ladders, lettered bean bags), and mentoring from the research team. Teachers in the TWM-E condition delivered three 40-min physically active English lessons per week for six weeks, whereas the control condition continued with the usual lessons. For both conditions, assessments occurred at baseline and post-test (six weeks). Children wore accelerometers on their wrists (Axivity) for one week during school time to measure their intensity of physical activity intensity (primary outcome). On-task behavior was assessed using a momentary time sampling procedure and expressed as a percentage of lesson time. Standardized tests were used to assess literacy skills (i.e., spelling, grammar and punctuation) and executive functioning (i.e, inhibition and task shifting). Results: No significant group differences were observed for physical activity outcomes, spelling or executive functions. Compared to the control group, the TWM-E group displayed improved on-task behavior (adjusted mean difference = 18.1% of lesson time, 95% CI [10.12 to 26.02], p < .001, d = 0.53), and improved grammar and punctuation scores (adjusted mean difference = 3.0, 95% CI [ 0.7 to 5.4], p = 0.018, d = 0.16). Conclusions: Despite minimal effect on overall physical activity levels, active lessons have important benefits for students’ on-task behavior and literacy.