In a method of operating a memory system, first security data and a first timestamp for preventing a replay attack are written by a host device to a first memory area which is an external memory area. A second timestamp is updated by the host device based on the first timestamp. The second timestamp corresponding to the first timestamp is stored in a second memory area distinguished from the first memory area. A first notification signal representing a result of updating the second timestamp is received by the host device. A writing operation for the first security data is completed when it is determined, by the host device, based on the first notification signal that the second timestamp is successfully updated.