In multi-FPGA prototyping systems for circuit verification, serialized time-multiplexed I/O technique is used because of the limited number of I/O pins of an FPGA. The verification time depends on a selection of inter-FPGA signals to be time-multiplexed. In this paper, we propose a method that minimizes the verification time of multi-FPGA systems by finding an optimal selection of inter-FPGA signals to be time-multiplexed. In the experiments, it is shown that the estimated verification time is improved 38.2% on average compared with conventional methods.