A storage system and method for enabling partial defragmentation are provided. In one embodiment, a storage system comprises a memory and a controller. The controller is configured to receive an indication from a host that the host will be reading from a portion of the memory in a burst mode; determine whether a fragmentation level of the portion of the memory is above a threshold; and in response to determining that the fragmentation level of the portion of the memory is above the threshold, perform a defragmentation of the portion of the memory prior to reading data stored in the portion of the memory. Other embodiments are provided.