A memory system may include a memory controller and a memory device including a plurality of sequential areas. The memory controller may control the performance of a background media scan (BGMS) operation on one or more sequential areas among the plurality of sequential areas. The memory controller may receive an open command for allocating a buffer to a sequential area among the plurality of sequential areas, where first time information corresponds to a time at which the open command is received by the memory controller. The memory controller may calculate a first period based on the first time information, and determine, based on the first period, a skip area in which the BGMS operation is skipped among the plurality of sequential areas for each of a plurality of BGMS periods.