In accordance with the present invention is provided a system and method for improving a timestamp precision in a precision timestamp protocol (PTP) device. The present invention provides for dynamic adjustment of otherwise uncertainty of the latency of a connection between two devices connected together through a gearbox and/or a block sync circuit. The dynamic adjustment is accomplished by identifying the alignment of data within the gearbox and block sync and adjusting the timestamp assigned to the data based upon the identified alignment to remove the jitter associated with the gearbox and the block sync, thereby improving the timestamp precision in the PTP device. In a particular embodiment, the invention is employed in a serial-deserializer (SERDES) device.