A synchronization timing loop detection method includes monitoring an active timing reference for a flapping event at a network element, incrementing a counter for each detected flapping event, determining if the counter exceeds a threshold over a predetermined time period, and, if the counter exceeds the threshold, declaring a possible timing loop on the active timing reference. The flapping event can include the active timing reference being active followed by inactive due to synchronization status messaging and one of a logical and physical timing loop on the active timing reference. A synchronization timing loop detection system and a network element for synchronization timing loop detection for the synchronization timing loop detection method are also disclosed.