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.

[1][2] His early education focused on theology, philosophy and the classics in preparation for an expected career as a minister.

However, when he entered Princeton University in 1873 at the age of fifteen, he became interested in science, especially geology, psychology, and chemistry.

[3] A course he took from the renowned Swiss geologist Arnold Guyot was a turning point in his career aspirations.

[5][6] Scott received numerous professional awards during his long career:[2] The pike cichlid fish Crenicichla scottii C. H. Eigenmann, 1907 was named in his honor.