The problem, which has been resolved, was located at Haymarket, and the knock-on effect is expected to continue to cause issues until at least 7pm.
The 17:16 Edinburgh to Kirkcaldy will be cancelled due to a shortage of train crew, along with a the 18:40 Edinburgh to Perth service.
However, ScotRail says the trains between Edinburgh and Glenrothes with Thornton are returning to normal but may be revised or delayed.
There have already been cancellations to some Fife services this morning and this afternoon, with all trains on the route subject to delay or revision.
A ScotRail Spokesman said: “The signal fault has been resolved. However, there will still be some disruption as we work to get services back on schedule.
“Given the level of disruption throughout the day, it will take a bit of time to get the service back to normal.
“There are still replacement buses and we are doing all we can to keep customers moving.
“Passengers should continue to check @ScotRail on Twitter or the ScotRail app for the most up to date information.”
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