The message comes after crew members reported numerous incidents where used tissues were left on the seats and tables in train carriages.
The issue has been more noticeable since the coronavirus pandemic.
A spokesman for the train company said: “We're seeing numerous reports from crews of dirty tissues being left on tables and seats.
“This isn't fair on anyone.
“Our Train Presentation teams regularly clean our bins - inside and out - so please use them.”
“Used tissues belong in the bin, don't leave them for someone else to find and deal with.
“Catch coughs and sneezes in a tissue. Bin it immediately. Wash your hands with soap and water for 20 seconds.
“Catch it. Bin it. Kill it.”
In response Traffic Scotland posted on twitter: “Come on folks, if you have to use public transport as a necessity please dont be doing things like this
“Its careless, reckless and dangerous to those Key Workers who are keeping the country running at the moment
“Pop those used tissues in the bin where they belong.”
ScotRail has recently reduced trains running amid the coronavirus outbreak.
In doing so, staff have had extra time between services to make sure the trains are extra clean before using.
Today the company pledged to add more services for key workers if needed and insisted overcrowding has been cut.
Those travelling plummeted by 80 per cent and 70 per cent on Monday compared to normal.