A number of train passengers and drivers were injured in such incidents on the Dhaka-Chittagong-Sylhet route last year.
Railway police DIG Kamrul Hasan said they were working to ensure that home-bound people were not attacked.
Commuters say they opt for train journeys to avoid traffic snarls during Eid but are worried about the hazards of trains being pelted with stones.
In August last year, university student Preeti Das was killed when a stone hit her while travelling in a train.
A Bangladesh Railway probe into the death failed to pin responsibility.
It had blamed ‘unidentified miscreants’ for the incident and said they might have hurled the stone "for fun".
The railway authorities have been running mass awareness campaigns to prevent such incidents.