Abstract : The concept of chemical supply chain has received increased attention in the process systems engineering community in the last decade. This chapter discusses the methods, tools, and applications, which are relevant to the pharmaceutical industry. Among the various supply chains that have been studied, pharmaceutical supply chains turn out to be very complex, due to several factors such as long development timelines, high attrition rates in drug development, resource-intensive operations, involvement of multiple stakeholders, among others. A fundamental challenge in managing a pharmaceutical company is identifying the optimal allocation of finite resources across the infinite constellation of available investment opportunities. Specific attention is given here to the modeling and optimization of three key phases in the life cycle of an innovative drug product, namely, product development pipeline management, capacity planning, and supply chain management. The state of the art in these domains is reviewed, some challenges are identified, and opportunities for further research effort are highlighted.