In longitudinal studies, measurement invariance is required to conduct substantive comparisons over time or across groups. In this study, we examined measurement invariance on a recently developed instrument capturing student preferences for seven instructional strategies related to science learning and career interest. We have labeled these seven instructional strategies as Collaborating, Competing, Caretaking, Creating/Making, Discovering, Performing, and Teaching. A better understanding of student preferences for particular instructional strategies can help educators, researchers, and policy makers deliberately tailor programmatic instructional structure to increase student persistence in the STEM pipeline. However, simply confirming the relationship between student preferences for science instructional strategies and their future career choices at a single time point is not sufficient to clarify our understanding of the relationship between instructional strategies and student persistence in the STEM pipeline, especially since preferences for instructional strategies are understood to vary over time. As such, we sought to develop a measure that invariantly captures student preference over a period of time: the Framework for Observing and Categorizing Instructional Strategies (FOCIS). We administered the FOCIS instrument over four semesters over two middle school grades to 1009 6th graders and 1021 7th graders and confirmed the longitudinal invariance of the FOCIS measure. This confirmation of longitudinal invariance will allow researchers to examine the relationship between student preference for certain instructional strategies and student persistence in the STEM pipeline.