The present disclosure provides a system and method for enabling a flexible PCIe topology in a computing system. The flexible PCIe topology can allow a user to adjust PCIe connections between CPUs and components of the computing system based upon a specific application. In some implementations, the computing system comprises a plurality of CPUs, a plurality of GPUs or Field-Programmable Gate Arrays (FPGAs), a plurality of PCIe switches, and a plurality of network interface controllers (NICs). In some implementations, the computing system comprises a switch circuit to connect the plurality of CPUs, the plurality of PCIe switches, and the plurality of NICs. The switch circuit comprises a plurality of inputs and a plurality of outputs to connect the plurality of CPUs, the plurality of PCIe switches and the plurality of NICs. Connection routes within the switch circuit can be adjusted to set a specific PCIe topology of the computing system.