Four trains were cancelled for all or part of their journey and others delayed.
The fault happened at Glenrothes with Thornton station shortly after 7am.
The ScotRail Alliance with Network Rail said two trains were cancelled and two were part cancellations, meaning they operated over only part of their journey.
The problem happened at 7:05am, preventing trains from running through the station, and was resolved around 7:45am.
A ScotRail Alliance spokesperson said: “Services in Fife were briefly disrupted this morning.
"We apologise to customers affected, and appreciate their frustration when delays happen.
“Compensation is available for customers who were delayed by 30 minutes or more.
"Simply keep hold of your ticket, and claim on the ScotRail website.”