Time transfer systems and methods in Flexible Ethernet (FlexE) include, in a node supporting Flexible Ethernet (FlexE), communicating a FlexE group with an adjacent node via a FlexE shim; providing a synchronization message channel to the adjacent node via overhead of the FlexE shim for the FlexE group; and exchanging synchronization messages via the synchronization message channel with the adjacent node. The synchronization messages can be Precision Time Protocol (PTP) messages. A timestamp point for a synchronization message can be a start of a FlexE frame or multi-frame boundary.