This paper presents a scheduling method that uses Petri net modeling and heuristic search to handle the tool setup. In manufacturing systems, a tool is attached to a particular machine to process a particular operation. The activity to attach a tool to a particular machine and detach the tool from the machine requires time. The processing time of operations varies according to the attached tool and the machine used. The method proposed in this paper uses Petri net to model these characteristics and applies a search algorithm to the reachability graph of the Petri net model to generate an optimal or near-optimal schedule. New heuristic functions are developed for efficient search. The experimental results that show the effectiveness of the proposed method are presented.