Health research is important for innovation and assessment of health status and health interventions, and maintaining a strong, engaged cohort of rural health researchers is essential for the ongoing improvement of the health of rural populations. Ethical guidelines and processes ensure research is undertaken in a way that protects and, where possible, empowers participants. We set out to systematically examine and document the challenges posed by ethics and governance processes for rural health researchers in Western Australia (WA) and the impact on the research undertaken. In this qualitative study, fifteen WA-based rural health researchers were interviewed. The identified challenges included inefficient systems, gatekeeping, apparent resistance to research and the lack of research experience of those involved in approval processes. For researchers seeking to conduct studies to improve rural and Aboriginal health, extended delays in approvals can hold up and impede research, ultimately changing the nature of the research undertaken and constraining the willingness of practitioners and researchers to undertake health research. Unwieldy ethics processes were seen to have a particularly onerous impact on rural research pertaining to service delivery, multiple sites, and research involving Aboriginal people, impeding innovation and inquiry in areas where it is much needed.