We consider problems of tool loading and scheduling in a flexible manufacturing system (FMS) in which tool transportation constitutes the major portion of material flows. In this type of FMSs, parts are initially assigned to machines and released to the machines according to input sequencing rules. Operations for the parts released to the machines are performed by tools initially loaded onto the machines or provided by an automatic tool transport robot when needed. For an efficient operation of such systems, therefore, we may have to consider loading and scheduling problems for tools in addition to those for parts. In this paper, we consider three problems, part loading, tool loading, and tool scheduling problems with the overall objective of minimizing the makespan. The part loading problem is solved by a method similar to that for the bin packing problem and then a heuristic based on the frequency of tool usage is applied for tool loading. Also suggested are part input sequencing and tool scheduling rules. To show the effectiveness of the overall algorithm suggested here, we compare it with an existing algorithm through a series of computational tests on randomly generated test problems