One embodiment of the present invention provides a system that facilitates changing a clock frequency in a memory system. During operation, the system receives a command to change the clock frequency to a new clock frequency. The system then iteratively changes the clock frequency to the new clock frequency. More specifically, the system starts an iteration by slewing the clock frequency toward the new clock frequency by an increment to reach an intermediate frequency without interfering with normal memory-system operation. Next, the system signals a memory controller to pause normal memory system operation by completing or cancelling all in-flight or outstanding memory system operations and not accepting additional memory operation requests. Upon receiving an acknowledgement from the memory controller that all in-flight or outstanding memory operations have completed or terminated, the system signals the memory controller to cause a delay-locked loop (DLL) inside the memory system to relock to the intermediate frequency. When the DLL relocks to the intermediate frequency, the system completes the iteration by resuming normal memory system operation.