A method and apparatus for optimizing a configuration memory of a reconfigurable processor is provided. The method of optimizing the configuration memory of the reconfigurable processor includes analyzing parallelism of a loop of a program code based on an architecture of the reconfigurable processor and information regarding the configuration memory, scheduling groups of function units (FUs) to be activated in each cycle of the loop based on the analyzed parallelism, generating configuration data of each cycle, and determining a memory mapping to store the generated configuration data in the configuration memory.