In educational research, there is a growing interest in functional magnetic resonance imaging (fMRI) to examine students' levels of processing. As there is a growing interest in the use of fMRI, a systematic review was conducted to examine how deep and surface levels of processing are operationalized within the neuroscientific field. In addition, we investigated how this operationalization impacts on the conceptualization of levels of processing within fMRI research. A systematic search was conducted within the MEDLINE, PubMed, ERIC, and Web of Science databases, and 25 studies were identified for this review. With regard to the operationalization, the review indicates that levels of processing were examined under highly controlled conditions with decontextualized and simplified language stimuli. Analysis of these studies revealed that there is a lack of conceptual clarity as, in half of the cases, no theoretical framework was explicitly mentioned, and no clear definition was given regarding levels of processing.