Introduction: The outcome of the effects of transitioning to minimalist running shoes is a topic of interest for runners and scientists. However, few studies have investigated the longer term effects of running in minimalist shoes. The purpose of this randomised controlled trial (RCT) is to investigate the effects of a 26 week transition to minimalist shoes on running performance and injury risk in trained runners unaccustomed to minimalist footwear. Methods and analysis: A randomised parallel intervention design will be used. Seventy-six trained male runners will be recruited. To be eligible, runners must be aged 18-40 years, run with a habitual rearfoot footfall pattern, train with conventional shoes and have no prior experience with minimalist shoes. Runners will complete a standardised transition to either minimalist or control shoes and undergo assessments at baseline, 6 and 26 weeks. 5 km time-trial performance (5TT), running economy, running biomechanics, triceps surae muscle strength and lower limb bone mineral density will be assessed at each time point. Pain and injury will be recorded weekly. Training will be standardised during the first 6 weeks. Primary statistical analysis will compare 5TT between shoe groups at the 6-week time point and injury incidence across the entire 26-week study period. Ethics and dissemination: This RCT has been approved by the Human Research Ethics Committee of the University of South Australia. Participants will be required to provide their written informed consent prior to participation in the study. Study findings will be disseminated in the form of journal publications and conference presentations after completion of planned data analysis. Trial registration number: This RCT has been registered with the Australian New Zealand Clinical Trials Registry (ACTRN12613000642785).