 Scott was born in Cincinnati, Ohio on February 12, 1858, the son of Mary Elizabeth Hodge Scott and William McKendree Scott, a Presbyterian minister.He was the youngest of three sons; his brother Hugh Lenox Scott went on to become superintendent of West Point and Army Chief of Staff.Shortly after the family moved to Princeton, New Jersey in 1861, his father died and the family lived with his maternal grandfather who was also a Presbyterian minister and an instructor at the Princeton Theological Seminary.