There will be no services from Glasgow Central to Ayr past Kilwinning until at least Monday.
The fire service was called to the blaze in Barassie Street – in the ticket office – around lunchtime on Saturday.
It took several hours to bring the fire under control. No-one was injured.
ScotRail the Fire Commander and British Transport Police closed the line immediately, and services between Glasgow Central and Ayr were suspended.
Much of the building on platform one has been destroyed and an overhead power cable damaged. The cause of the fire is unknown.
Emergency services were still at the scene on Saturday night and a cordon has been set up around the building.
On Sunday, a restoration group offered £500,000 to help repair the building, according to reports on the BBC.
The Railway Heritage Trust said it wanted to help salvage the Victorian structure, which opened in 1892 and was designed by architect James Miller.
A nearby hairdressing salon and café are understood to also have been damaged.
ScotRail organised replacement bus services from Ayr, Largs, Kilmarnock and Troon stations to transport people who had already completed the outward leg of their journey before the fire broke out, back to Kilwinning station.
From there they were able to transfer to a shuttle train service to Glasgow Central. Several hundred passengers were affected.
ScotRail is working on an appropriate contingency timetable that will see services terminate at, and start back from, Kilwinning.
It is likely there will be two services an hour between Glasgow and the Ayrshire town.
The Glasgow – Largs/Ardrossan services are running.
ScotRail is also advising customers to closely monitor its Twitter feed for the most up-to-date information on the running of services over the next few days.
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