Model‐based systems engineering (MBSE) is part of a long‐term trend toward model‐centric approaches adopted by many engineering disciplines. We establish the need of an MBSE approach by reviewing the importance, complexity, and vulnerability of the U.S. chemical supply chains. We discuss the origins, work processes, modeling approaches, and supporting tools of the systems engineering discipline (SE) and discuss limitations of the Process Systems Engineering (PSE) framework. We make the case for MBSE as a more generalizable approach. We introduce systems modeling strategies for MBSE, and a novel MBSE method that supports the automation tailored and extended to support the analysis of chemical supply chains. We demonstrate a specific use case of this method by creating a systems model for the manufacturing of an active pharmaceutical ingredient, Atropine. We conclude with a prospectus on developmental opportunities for extracting greater benefit from MBSE in the design and management of chemical supply chains.