The police have arrested a 22-year-old over the incident.
The Vande Bharat train was en route to Lucknow from Dehradun when the stones were hurled at it near Kharanja Qutubpur village on the Laksar-Moradabad railway section, the police said.
One of the windows of Coach 6 developed a large crack.
The loco pilot informed the control room in Moradabad and the information was passed on to the Railway Police Force (RPF).
A team from the RPF reached Kharanja Qutubpur village and arrested 22-year-old Salman after making inquiries.
A case has been registered against the accused.