There is an increasing trend in the chemical process industry to operate flexible batch plants because of their capability to manufacture multiple products simultaneously by sharing the same process resources. In this paper, the scheduling of multi-purpose batch chemical plants with junction (header) constraints is considered. A mixed-integer non-linear model for the scheduling of multi-purpose batch chemical plants is formulated that considers the connection between equipment sets, transfer times, variable batch sizes, alternative process plans, and batch merging. Because of the computational time complexity of the batch scheduling problem, a heuristic scheduling algorithm that minimizes the total tardiness is developed lo solve the model.