Methods and apparatus for partitioning a microprocessor pipeline to support pipelined branch prediction and instruction fetching of multiple execution threads. A thread selection stage selects a thread from a plurality of execution threads. In one embodiment, storage in a branch prediction output queue is pre-allocated to a portion of the thread in one branch prediction stage in order to prevent stalling of subsequent stages in the branch prediction pipeline. In another embodiment, an instruction fetch stage fetches instructions at a fetch address corresponding to a portion of the selected thread. Another instruction fetch stage stores the instruction data in an instruction fetch output queue if enough storage is available. Otherwise, instruction fetch stages corresponding to the selected thread are invalidated and refetched to avoid stalling preceding stages in the instruction fetch pipeline, which may be fetching instructions of another thread.