In described embodiments, a multiple first-in, first-out buffer pointers (multi-FIFO pointers) alignment system includes synchronization circuitry to align multiple FIFO buffer operations. A FIFO read clock stoppage signal is generated by master logic that stops the read clock shared by all the transmit channels and then re-starts the read clock to align them. The FIFO read clock stoppage signal is applied to the read clock of all FIFOs which need to be aligned and, when rate change is needed, the FIFO read clock stoppage signal suspends the read clock, causing local write and read pointers to be reset. After the FIFO read clock stoppage signal is de-asserted, the read clock starts to all FIFOs concurrently, thereby aligning the channels.