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Background School-based physical education is an important public health initiative as it has the potential to provide students with regular opportunities to participate in moderate-to-vigorous physical activity (MVPA). Unfortunately, in many physical education lessons students do not engage in sufficient MVPA to achieve health benefits. In this trial we will test the efficacy of a teacher professional development intervention, delivered partially via the Internet, on secondary school students’ MVPA during physical education lessons. Teaching strategies covered in this training are designed to (i) maximize opportunities for students to be physically active during lessons and (ii) enhance students’ autonomous motivation towards physical activity. Method A two-arm cluster randomized controlled trial with allocation at the school level (intervention vs. usual care control). Teachers and Year 8 students in government-funded secondary schools in low socio-economic areas of the Western Sydney region of Australia will be eligible to participate. During the main portion of the intervention (6 months), teachers will participate in two workshops and complete two implementation tasks at their school. Implementation tasks will involve video-based self-reflection via the project’s Web 2.0 platform and an individualized feedback meeting with a project mentor. Each intervention school will also complete two group peer-mentoring sessions at their school (one per term) in which they will discuss implementation with members of their school physical education staff. In the booster period (3 months), teachers will complete a half-day workshop at their school, plus one online implementation task, and a group mentoring session at their school. Throughout the entire intervention period (main intervention plus booster period), teachers will have access to online resources. Data collection will include baseline, post-intervention (7–8 months after baseline) and maintenance phase (14–15 months after baseline) assessments. Research assistants blinded to group allocation will collect all data. The primary outcome will be the proportion of physical education lesson time that students spend in MVPA. Secondary outcomes will include leisure-time physical activity, subjective well-being, and motivation towards physical activity. Discussion The provision of an online training platform for teachers could help facilitate more widespread dissemination of evidence-based interventions compared with programs that rely exclusively on face-to-face training. Trial registration Australia and New Zealand Clinical Trials Registry-ACTRN12614000184673. Registration date: February 19, 2014. Electronic supplementary material The online version of this article (doi:10.1186/s12889-015-2583-7) contains supplementary material, which is available to authorized users.