The train operator said the damage had forced needless cleaning work during the Covid-19 crisis when hundreds of its staff have been forced to stay home.
The incident happened while the train was parked at Wemyss Bay station on Sunday night.
Pictures of the graffiti while the train was at Glasgow Central station yesterday have been posted on social media.
The class 385 electric train will now have to be taken out of service for the paint to be removed.
A ScotRail spokesperson said: “As noble as the message may be, this is vandalism. It has absolutely no place on Scotland’s Railway, and expends valuable cleaning time unnecessarily.”
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