The reward is available to anyone who provides information which leads to a conviction following the incident on Monday 22 June.
A British Transport Police (BTP) investigation is already underway, and the train operator has now stepped in to help appeal for further information.
Chris Jackson, Regional Director at Northern, said: “This was a shocking incident in which a stone was thrown from a bridge, smashing the driver’s cab window and causing minor injuries to the driver.
“Thankfully the driver has made a full recovery, but it is only through good fortune that this was not a much more serious incident.”
The incident happened at 6.30pm on Monday 22 June as the train was passing through an area of railway near to Clegg Hall Lane between Smithy Bridge and Rochdale stations.
Chris added: “Officers investigating the incident believe a man wearing a red hoody threw the stone and I am now appealing to any with information about this to come forward. Someone will know who did this and we need to find them before they do something similar which may have far worse consequences.
Anyone with information can contact BTP by texting 61016 or by calling 0800 40 50 40. In both cases, quote reference number 2000041927.
Alternatively, people can call Crimestoppers, anonymously, on 0800 555 111.