Scott was born in Lanark County, Ontario in what was then Upper Canada to Irish immigrant parents.
His father died when he was an infant, and the family moved to Perth, Ontario where Scott attended school and then apprenticed as a printer.
During the Red River Expedition of 1870, Scott – by this time a colonel – was in command of the Ontario Rifles which arrived at Fort Garry following Louis Riel's escape.
In 1874, he retired from military service but remained in Manitoba where he entered politics and was elected to Winnipeg's first city council; he became mayor in 1877.
In 1878, he was elected to the Manitoba legislature from the district of Winnipeg and, in 1880, he defeated incumbent Donald A. Smith to become the Conservative MP for Selkirk.