Scott was born in Leith, near Edinburgh, the eldest son of Reverend George Scott, a Minister in the church at Dairsie and Mary Forsyth, daughter of the Edinburgh advocate Robert Forsyth.[1]
Scott was educated at the High School, Edinburgh, then in Stuttgart before becoming a student at University College, London. In 1870, while a student at University College, London, he was awarded a Whitworth Exhibition. He went on to read mathematics at St John's College, where he was fourth wrangler in the Tripos in 1875 and was elected to a fellowship in 1877.[2][3]
After publishing The Theory of Determinants and Their Applications in 1880, Scott turned his attention to the law, become a barrister in 1883, and to institutional history, including histories of St. John's College, Cambridge, published between 1882 and 1907.[1][3]
In 1908 he was appointed as the Master of St John's College, a position he held until his death in Cambridge in 1933, and from 1910 to 1912 he served as Vice-chancellor of the University. On his death he left the library of St John's one of the largest collection of Burmese manuscripts in Europe.[3]