In today’s knowledge economies, a significant part of academic research is funded by national research funding institutes. Research funding institutes commonly design national research agendas in an attempt to define the optimal course of research and implement them using funding strategies where some funding is locked behind thematic conditions. By enforcing research agendas, however, research funding institutions interfere with researchers’ academic freedom. This research studies the relationship between researchers’ freedom and research agendas through Amartya Sen’s freedom of choice concept and Patrick Suppes’ measure of freedom of choice. By focusing on the relationship between choices in research direction and thematic grants, this study examines how research agendas of the Dutch Research Council (NWO) influence the freedom of choice of researchers. This study also investigates the philosophical conceptions of academic freedom of Immanuel Kant, Wilhelm von Humboldt, and John Stuart Mill and compares them with freedom of choice to determine the compatibility of research agendas. This research applies the measure of freedom of choice on NWO’s own funded projects to determine how NWO supports researchers’ freedom of choice. The findings confirm NWO’s own documentation regarding their strategies for increasing researcher freedom. Additionally, the research highlights difficulties and potential improvements in the application of freedom of choice and its measure. Based on freedom of choice and academic freedom, this study derives and studies policy strategies for increasing researchers’ freedom and allowing for the design of research agendas with academic freedom in mind. Ultimately, this study presents a theoretical approach to policy regarding research agendas and underscores the importance of research freedom and academic freedom in NWO’s ability to create the right research environments for impactful and innovative academic research.