A secure FC NVMe fabric communications system includes a host device having host WWPNs associated with each of its host NQNs, an NVMe target device having a target WWPNs associated with each of its target NQNs, and FC networking device(s) that couple the host device to the NVMe target device. The FC networking device(s) perform, for each host WWPN associated with the host NQNs, host login operations that register the host NQN for that host WWPN as an NVMe host, and perform, for each target WWPN associated with the target NQNs, target login operations that register the target NQN associated with that target WWPN as an NVMe target. The FC networking device(s) then provide, to the host for each host NQN, target NQN details for target NQN(s) zoned for communication with that host NQN to allow respective communication session(s) to be established between the host NQN and those target NQN(s).