An unavailable memory device initialization system includes a memory controller device that is configured to determine whether a memory system includes unavailable memory devices during initialization operations. During the first initialization operations, a BIOS engine identifies unavailable memory device(s) in the memory system that were determined to be unavailable by the memory controller device during the first initialization operations and, in response, stores respective unavailable memory device identifier(s) associated with each unavailable memory device in a non-volatile storage subsystem. Subsequently, during second initialization operations and based on the respective unavailable memory device identifier(s) stored in the non-volatile storage subsystem, the BIOS engine generates a memory overlay that hides each unavailable memory device from the memory controller device such that the memory controller device determines that the memory system does not include any unavailable memory devices during the second initialization operations.