—Due to increase in demand for reconfigurability in embedded systems, real-time task scheduling is challenged by non-negligible reconfiguration overheads. If such overheads are not considered, tasks may not be schedulable under given deadlines, and hence, affecting the quality of service. We introduce the problem of real-time periodic task scheduling under transition overhead on heterogeneous reconfigurable systems. We formulate the problem as a network flow problem and provide a mixed integer linear programming solution. We compare our proposed solution with optimal scheduling under maximum fixed transition overhead. We deployed our method on task scheduling for multiple communication protocols on reconfigurable FPGA-like systems. Results show that our proposed scheduling improves the task schedulability by 24.2% in comparison with non-preemptive EDF and by 17.5% in comparison with maximum-transition-overhead scheduling. Keywords- Dynamically reconfigurable systems and Real-time tas...