A method and an apparatus for operating a multi-processor system of an electronic device. The electronic device includes a memory for storing commands for running a secure Operating System (OS) and a non-secure OS, and at least one processor including a plurality of processor cores. Upon generation of at least one secure OS thread in the secure OS installed on the electronic device, the at least one processor generates and sends information indicating a secure mode operation request by assigning at least one of the processors cores in the secure OS, and executes the secure OS thread on the at least one processor core assigned in a secure mode based on the information.