This paper proposes methods of computing maximum throughput for Petri nets that model workflows including resources, called WF-nets with resources. We first propose the formal definitions of WF-nets with resources and their subclasses: marked graph/state machine WF-nets with conflict-free resources (CF-Res-MG/SMWF-nets). We also show several properties of CF-Res-MG/SMWF-nets. Next we give the methods of computing maximum throughput for CF-Res-MG/SMWF-nets under condition that all tokens have to be processed in the order of First-In First-Out (FIFO). Concretely, for CF-Res-MGWF-nets, on the basis of Ramamoorthy's method of computing cycle time, we give an algorithm of computing maximum throughput under the FIFO condition. For CF-Res-SMWF-nets, there is not any method of computing maximum throughput under the FIFO condition. So we are the first to give an algorithm of computing maximum throughput for CF-Res-SMWF-nets under the FIFO condition. Finally we show an example of computing maximum throughput by using our method.