Systems and methods for Physical Coding Sublayer (PCS) encryption implemented by a first network element communicatively coupled to a second network element include encrypting a Flexible Ethernet (FlexE) signal based on a first encryption key with encryption applied to a 64b/66b bit stream associated with the FlexE signal at one or more of a FlexE client layer and a FlexE shim layer; switching to a second encryption key at a predetermined point in the FlexE signal; and encrypting the FlexE signal with the second encryption key subsequent to the switching.