Over the last decade, a large number of research papers, certified courses, professional development programs and scientific conferences have addressed supply chain management (SCM), thereby attesting to its significance and importance. SCM is a multi-criteria decision-making (MCDM) problem because throughout its process, different criteria related to each supply chain (SC) activity and their associated sub-criteria must be considered. Often, these criteria are conflicting in nature. For their part, MCDM methods have also attracted significant attention among researchers and practitioners in the field of SCM. The aim of this chapter is to conduct a systematic literature review of published articles in the application of MCDM methods in SCM decisions at the strategic, tactical and operational levels. This chapter considers major SC activities such as supplier selection, manufacturing, warehousing and logistics. A total of 140 published articles (from 2005 to 2017) were studied and categorized, and gaps in the literature were identified. This chapter is useful for academic researchers, decision makers and experts to whom it will provide a better understanding of the application of MCDM methods in SCM, at various levels of the decision-making process, and establish guidelines for selecting an appropriate MCDM method for managing SC activities.