An endpoint device discovery system includes a downstream port. A register is coupled to the downstream port. An endpoint ready status bit may be set in the register in response to an endpoint ready message received at the downstream port. A non-transitory computer-readable medium is coupled to the register and includes computer-readable instructions that, when executed by a processor, cause the processor to determine that the endpoint ready status bit is set and, in response, configure an endpoint device that is coupled to the downstream port. The endpoint device discovery system may be included in an information handling system (IHS) in order to provide for discovery of endpoint devices that are coupled to the IHS as soon as those endpoint devices have initialized.