In machine job shops with automated guided vehicles(AGVs) as mean of transportation of job parts, it’s usually hard to determine the optimal fleet size of AGVs for achieving a desired performance. In this paper, a heuristic AGV dispatching algorithm is constructed based on the concept of ideal pipeline and Petri Net theory to balance the job part sheduling and AGV dispatching that minimize the number of AGVs for achieving zero idle time of the machine. The problem is formulated as polynomial equations owing to the mathematical property of Petri Net and since obtaining the optimal solutioin is computational difficult, a way to circumvent the difficulty is necessary for the real application of the algorithm. A heuristic dispatching algorithm that schedules the dispatch of AGVs on a selected window basis is used to reduce the computation time and makes the dispatching algorithm capable of real time implementation.