A system and method for masking a hardware boot sequence 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. Such masking may involve running the same boot code as the boot processor but without obtaining access to security information, such as the security key for accessing the system. The electromagnetic and/or thermal signatures generated by the execution of the masking code preferably approximate the electromagnetic and/or thermal signatures of the actual boot code executing on the boot processor. In this way, it is difficult to distinguish which processor is the actual boot processor.