Described is a system and method that facilitates fast and reliable synchronization of computer/file system directories. A synchronization (FastSync) subsystem operates in a discovery/enumeration phase to provide a calling client with a set of the differences between directories, and then operates in an action phase to perform operations as directed by the client to synchronize the different directories. The discovery/enumeration and action phases use parallel operation and I/O (input/output) pipelining. Multiple threads are used during enumeration to enumerate each directory's children, and enqueues each sub-directory to be handled by a new thread. During the action phase, when an operation is requested, the FastSync subsystem packages up the operation, item pointer, and context information into an internal context block and queues that packet as a work item for a process thread pool to handle.