This doctoral dissertation work aims to provide a discrete-event system-based methodology for design, implementation, and operation of flexible and agile manufacturing and demanufacturing systems. After a review of the current academic and industrial activities in these fields, a Virtual Production Lines (VPLs) design methodology is proposed to facilitate a Manufacturing Execution System integrated with a shop floor system. A case study on a back-end semiconductor line is performed to demonstrate that the proposed methodology is effective to increase system throughput and decrease tardiness. An adaptive algorithm is proposed to deal with the machine failure and maintenance. To minimize the environmental impacts caused by end-of-life or faulty products, this research addresses the fundamental design and implementation issues of an integrated flexible demanufacturing system (IFDS). In virtue of the success of the VPL design and differences between disassembly and assembly, a systematic approach is developed for disassembly line design. This thesis presents a novel disassembly planning and demanufacturing scheduling method for such a system. Case studies on the disassembly of personal computers are performed illustrating how the proposed approaches work.