Systems and methods for time synchronization for clocks separated by a communication link allow a master clock to be positioned at a downstream-facing port or an upstream-facing port and to send synchronization commands with an associated time stamp embedded in transport layer protocol (TLP) prefixes to a slave clock. The slave clock may update its time value based on the received time stamp. Further, the slave may calculate a round trip delay between the master clock and the slave clock and use this delay calculation to correct the slave clock. The delay calculation may likewise be made using TLP prefixes. By using TLP prefixes in this fashion, the time synchronization can piggyback on existing message traffic, which reduces signaling overhead. Likewise, by using the TLP prefixes, the time synchronization may be initiated from either an upstream-facing port or a downstream-facing port.