Teacher agency has increasingly been acknowledged as an essential factor in advancing teachers’ professional development, shaping teachers’ professional identities and decision-making processes. However, a comprehensive empirical understanding of teacher agency remains limited. Drawing on the concept of teacher agency, this study aims to gain a comprehensive understanding of how (if at all) science teachers develop their agency and agentic practice in the pedagogy of scientific argumentation over time. Three science teachers with expertise in science education participated in this longitudinal study conducted over a 2-year period. Data were collected through video recordings of classroom practices, audio recordings of lesson planning meetings and teachers’ reflective interviews. A comparative case study analysis revealed that while all three teachers exhibited some degree of developments in teachers’ sense of purpose, mastery, autonomy to act and reflexivity while enhancing the pedagogy of scientific argumentation, the extent of this development varied among them. The framework provided a basis for illustrating how the concept of teacher agency can serve as a valuable tool for evaluating the pedagogical development. It would be interesting to identify factors that either support or hinder the development of teacher agency in science teaching for future research.