Currently, there is significant interest being directed towards the development of STEM education to meet economic and societal demands. While economic concerns can be a powerful driving force in advancing the STEM agenda, care must be taken that such economic imperative does not promote research approaches that overemphasize pragmatic application at the expense of augmenting the fundamental knowledge base of the discipline. This can be seen in the predominance of studies investigating problem solving approaches and procedures, while neglecting representational and conceptual processes, within the literature. Complementing concerns about STEM graduates’ problem solving capabilities, raised within the pertinent literature, this paper discusses a novel methodological approach aimed at investigating the cognitive elements of problem conceptualization. The intention is to demonstrate a novel method of data collection that overcomes some of the limitations cited in classic problem solving research while balancing a search for fundamental understanding with the possibility of application. The methodology described in this study employs an electroencephalographic (EEG) headset, as part of a mixed methods approach, to gather objective evidence of students’ cognitive processing during problem solving epochs. The method described provides rich evidence of students’ cognitive representations of problems during episodes of applied reasoning. The reliability and validity of the EEG method is supported by the stability of the findings across the triangulated data sources. The paper presents a novel method in the context of research within STEM education and demonstrates an effective procedure for gathering rich evidence of cognitive processing during the early stages of problem conceptualization.