Background Hospitals are common recruitment sites for injury and disability studies. However, the clinical and rehabilitation environment can create unique challenges for researchers to recruit participant populations. While there is growing injury and disability focused research involving Indigenous people to understand the types of services and supports required by this population to enhance their recovery experiences, there is limited knowledge of researchers’ experiences implementing recruitment processes in the tertiary hospital environment. This paper reflects on the specific challenges of recruiting Indigenous patients following a traumatic brain injury from two tertiary hospitals in Northern Australia. Methods Between July 2016 and April 2018, research staff recruited eligible patients from one hospital in Queensland and one hospital in the Northern Territory. Qualitative records summarising research staff contact with patients, family members and clinical hospital staff were documented. These qualitative records, in addition to field trip notes and researcher reflections were reviewed to summarise the main challenges in gaining access to patients who fit the eligibility criteria. Results During the recruitment process, there were five main challenges encountered: (1) Patients discharging against medical advice from hospital; (2) Discharge prior to formal emergence from Post Traumatic Amnesia as per the Westmead Post Trauma Amnesia Scale; (3) Patients under adult guardianship orders; (4) Narrow participant eligibility criteria and (5) Coordinating around patient commitments and treatment. Details of how the recruitment processes were modified throughout the recruitment phase of the study to ensure greater access to patients that met the criteria are described. Conclusion Based on our recruitment experiences, several recommendations are proposed for future TBI studies with Indigenous Australians. In addition to treatment, Indigenous TBI patients have wide range of needs that must be addressed while in hospital. Patient engagement and data collection processes should be flexible to respond to patient needs and the hospital environment. Employment of a centralized recruiter at each hospital site may help to minimise the challenges researchers need to navigate in the hospital environment. To improve recruitment processes in hospitals, it is essential for researchers examining other health or injury outcomes to describe their recruitment experiences.