A system and method for masking a boot sequence by running different code on each processor of a multiprocessor system are provided. With the system and method, one of the processors of a multiprocessor system is chosen to be a boot processor. The other processors of the multiprocessor system execute masking code that generates electromagnetic and/or thermal signatures that mask the electromagnetic and/or thermal signatures of the actual boot processor. The masking code executed by each of the non-boot processors may be different from each other and may be randomly selected from a plurality of masking code sequences stored in a masking code storage device. Each execution of masking code on each of the non-boot processors may generate a different electromagnetic and/or thermal signature such that none of the processors appear to be unique from an external monitoring perspective.