A system and method for synchronizing multiple backplanes within an information handling system are disclosed. An information handling system includes a first controller that may be operable to generate a time command at a predetermined time interval. A backplane including a second controller is communicatively coupled to the first controller. The second controller may be operable to receive the time command from the first controller and calculate a skew for the time command based at least on a location of the backplane. The second controller may further be operable to adjust a time domain of the backplane based on the calculated skew for the time command to synchronize the backplane.