Although the use of brain imaging techniques, such as functional magnetic resonance imaging (fMRI) is increasingly common in educational research, only a few studies regarding science learning have so far taken advantage of this technology. This paper aims to facilitate the design and implementation of brain imaging studies relating to science learning by presenting the epistemological and methodological framework of an ongoing fMRI study trying to identify brain mechanisms related to conceptual change in electrical concepts. To achieve this goal, we propose a review of literature, in the first part of this paper, to explain why we choose to study conceptual change using fMRI. In the second part, we present the methodology of an ongoing study to show how brain imaging can be applied in science education research. (Contains 1 figure.)