This paper focuses on the ethical tensions seen in health systems research by researchers owing to their scientific obligations to their research, ethical obligations to study participants, and social obligations to the community. Health systems research differs from other public health research fields in terms of the participants selected, power relations within health systems and the socio-political environment. The study seeks to answer the following questions through experiences in health system research. 1. What are the ethical tensions experienced by researchers in field work? 2. How are the existing guidelines used in resolving tensions arising in field work in India? To understand these ethical tensions, the World Health Organization’s Ethical Considerations for Health Policy and Systems Research were applied to research conducted in the health system settings. These tensions faced by researchers are explained through four emerging themes: the researcher’s position in the health system; voluntariness of participation: participation; and social justice.