The machine fell over near the village of Portgower in Sutherland.
The A9 between Helmsdale and Brora was closed in both directions for several hours to allow recovery work to take place while train services between Inverness and Wick also faced disruptions.
Network Rail said: “A road crane has come off the A9 road and is on the track near Helmsdale at Portgower.
“Network Rail will carry out an assessment of the damage caused after this last service has run. It is hoped a full service will be able to run in the morning.”