Methods and apparatus for providing in-order delivery in Fibre Channel (FC) fabric are disclosed. A topological change between a first switch and a second switch is evaluated to determine whether the topological change may result in out-of-order delivery. If it is determined that the topological change may result in out-of-order delivery, a flush frame is sent to the second switch and stop-on-mark is performed on all interfaces of affected links. Upon receiving the flush frame, the second switch drains all virtual output queues (VOQs) and sends an acknowledgement frame to the first switch. The first switch resumes in-order-delivery in an affected link after receiving the acknowledgement frame or expiration of a lifetime time of a frame.