Abstract Background There are many demonstrated benefits for health service organizations engaging in research. As a result, growing numbers of clinicians are being encouraged to pursue research as part of their clinical roles, including in allied health (AH). However, while the benefits of having clinician researchers embedded in AH services have been well established, the career needs of those engaged in these dual roles are poorly understood. The aim of this study was to examine perspectives of the career pathway for AH clinicians engaged in “clinician researcher” roles within Australian health services. Methods A qualitative descriptive study was conducted, utilizing semi-structured interviews. Purposive sampling was used to ensure selection of varied locations, professions and role types. Results were analysed using thematic analysis. Trustworthiness was established using regular peer debriefing during theme development, and respondent validation of final themes. Results Fifty-seven AH clinician researchers, including those who did and did not have research as a formal component of their current role, participated in semi-structured interviews. Key themes were as follows: (1) clinician researchers prefer roles which are embedded in health services; (2) current opportunities for clinician researcher roles in health are insufficient; (3) there are deficiencies in the pathway for clinician researcher careers; (4) clinician researchers are not always valued or incentivized by health services; (5) the current career challenges impair the viability of clinician researcher careers; and (6) the clinician researcher career path has been improving, and there is hope it will continue to improve. Conclusion This study outlines a number of weaknesses in the current career structure and opportunities for AH clinician researchers in Australian health services. In particular, while there are strong intrinsic drivers to pursue this dual career, extrinsic drivers are poorly developed, including a lack of job opportunities, an unstable career pathway and a lack of valuing or incentivizing this career choice within health services. This often means that clinician researchers feel compelled to choose between a research or clinical career, leading to loss of this valuable combined skill set. The findings of this research may assist health services in developing and supporting improved clinician researcher career pathways.