The system was getting back to its regular service for the afternoon rush, spokesman Sal Arena said Friday afternoon.
PATH train service has resumed with delays on the Journal Square-33rd Street and Hoboken-33rd Street lines.
Three LIRR train runs were canceled during the Wednesday evening rush, due to broken rail west of Rockville Centre.
C line subway service was completely shut down in both directions Monday evening, due to a broken rail in Brooklyn.
PATH trains are rolling again between New Jersey and New York City after repairs were made to a broken rail.