A secure processor with fault detection has a core thread which executes with a redundant branch processor thread. In one configuration, the core thread is operative on a fully functional core processor configured to execute a complete instruction set, and the redundant branch processor thread contains only initialization instructions and flow control instructions such as branch instructions and is operative on a redundant branch processor which is configured to execute a subset of the complete instruction set, specifically a branch control variable initialization and a branch instruction, thereby greatly simplifying the redundant branch processor architecture. Fault conditions are detected by comparing either a history of branch taken/not taken and branch targets, or a comparison of program counter activity for the core thread and redundant branch processor thread.