Introduction: The inequity of randomising participants to control groups in randomised controlled trials (RCTs) is often considered inappropriate, especially for research trials that include vulnerable populations such as Indigenous peoples. The Aboriginal and Torres Strait Islander Women's Fitness Program conducted a trial that randomly assigned participants to ' active' and 'waitlisted' groups. This paper reports on participant views of the randomisation protocol. Methods: A pragmatic RCT was conducted in an urban setting to assess the effectiveness of the 12-week Aboriginal and Torres Strait Islander Women's Fitness Program on metabolic health outcomes and waist circumference. Qualitative interviews were conducted at follow-up, one of the objectives was to explore participant perspectives on the research protocol, including participant randomisation to 'Active' and ' Waitlisted' groups. Results: A total of 49 interviews were conducted (26 Active and 23 Waitlisted participants). Two key factors influenced participant views on the protocol: 1) group assignment; and 2) how well they understood the research design, including the justification for randomisation. 'Active ' participants were concerned about the inequity of the randomisation process but overall supported the study protocol. Although most Waitlisted participants were disappointed about having to wait 12-months for the program, some participants derived motivation from being waitlisted, whilst others lost motivation. Well-informed participants were more likely to express both support for the randomisation process and an understanding of the research benefits than participants not attending an information session prior to registration. Conclusions: Participants were more accepting of the research protocol if it was clearly explained to them, if they understood the randomisation process and felt the randomisation was justified in terms of the potential for the results to benefit other Aboriginal and Torres Strait Islander women. Our study suggests that the time and resources required to adequately explain the research protocol in research trials should not be undervalued. Trial registration: Australian New Zealand Clinical Trials Registry (ACTRN12610000224022).