With the introduction of the European Health Data Space (EHDS), the secondary use of health data for research purposes is set to rapidly escalate. Secondary health data processing promises to address novel research questions, inform the design of future research and improve healthcare delivery generally. To comply with the existing data protection regulations, the secondary data use must be fair to individuals, among other things. However, there is no clear understanding of what fairness means in the context of secondary use of health data for scientific research purposes. In response, we conducted a scoping review of argument-based literature to explore how fairness for the individuals in the secondary use of health data has been conceptualized. Our review has revealed that balancing individual and public interests, reducing power asymmetries, setting conditions for commercial involvement and implementing benefit sharing were essential to guarantee fair secondary use research for individuals. The findings of this review can inform current and future research practices and policy development in order to adequately address concerns about fairness in the secondary use of health data.