Described are embodiments of methods, apparatuses, and systems for time synchronization of a multi-protocol I/O interconnect of computer apparatus. A method for synchronizing time across the multi-protocol I/O interconnect may include determining a first local time at a first port of a first switch of a switching fabric of a multi-protocol interconnect and a second local time at a second port of a second switch of the switching fabric, calculating an offset value based at least in part on a difference between the first local time and the second local time, and adjusting the second local time by the offset value. Other embodiments may be described and claimed.