In modern manufacturing systems with computational complexities, decision-making with respect to dynamic rescheduling and reconfiguration in case of internal disturbances is an important issue. This paper introduces a multi-agent-based dynamic scheduling system for manufacturing flow lines (MFLs) using the Prometheus methodology (PM) considering the dynamic customer demands and internal disturbances. The PM is used for designing a decision-making system with the feature of simultaneous dynamic rescheduling. The developed system is implemented on a real MFL of a small- and medium-sized enterprise (unplasticized polyvinyl chloride (uPVC) door and window) where the dynamic customer demands and internal machine break downs are considered. The application has been completely modeled using a Prometheus design tool, which offers full support to the PM, and implemented in JACK agent-based systems. Each agent is autonomous and has an ability to cooperate and negotiate with other agents. The proposed decision-making system supports both static and dynamic scheduling. A simulation platform for testing the proposed multi-agent system (MAS) is developed, and two real scenarios are defined for evaluating the proposed system. The analysis takes into account the comparisons of the overall performances of the system models using the MAS scheduling and conventional scheduling approaches. The result of simulation indicates that the proposed MAS could increase the uptime productivity and the production rate of flexible flow-line manufacturing systems.