YOBS halted a train passing through Wigan on Saturday when a brick was thrown through the driver’s cab window.
The Northern Rail train to Southport was forced to stop for 15 minutes and the driver sustained injuries which required hospital treatment.
It is the second time this month that missiles have been thrown at moving trains passing through the Gathurst area.
British Transport Police (BTP) said it was “vital” that they find the culprits to prevent further offences.
Sgt Andy Tomkins said: “This was an incredibly dangerous act which left the driver with injuries to his elbow.
“Officers will be stepping up patrols in the surrounding area to catch and deter criminal activity in the coming weeks.”
Passengers who were on the 4.46pm Manchester Victoria to Southport service reported hearing the impact before the train came to a halt just outside Gathurst.
Kathryn Gurney, 32, from Shevington, said: “We stopped around the Crooke area near to Gathurst and the driver got out of his cab and told us what happened.
“He said it was quite a common occurrence on that stretch.
“He came back to say we would continue to Southport despite the broken window. “When I got off at Gathurst, I saw that the window had been completely smashed by the brick.”
Passengers were showered with glass on June 8 when a piece of ballast was thrown at a moving train in a similar incident just past Ackhurst Crossing.
A male passenger was left with cuts to his forehead and ear.
BTP officers are now appealing for witnesses to come forward for both incidents.
Sgt Tomkins added: “We take this type of offence extremely seriously and it is vital that we identify the person responsible for this mindless act.”
Northern Rail director Lee Wasnidge said: “An incident such as this can cause serious shock and upset as well as potential physical injury to members of our train crew.
“The driver suffered painful injury and the damaged window meant the train had to be taken out of service for repair.
“I would urge anyone with information on this to contact our colleagues at BTP immediately.”
To contact BTP, call 0800 40 50 40, text on 61016 or contact Crimestoppers on 0800 555 111.