Scott received a baccalaureate degree from Yale College in 1869 and earned a Master of Arts (M.A.)

[3] According to historian Hugh Hawkins, Scott preferred teaching at Hopkins to his work with Bancroft.

[2][5] In 1883, Scott was appointed to the faculty of Rutgers College as a professor of history, political economy, and constitutional law, and was elected to succeed Merrill Edward Gates in 1891.

During Scott's tenure at Rutgers, Robert Francis Ballantine (1836–1905), a wealthy brewer from Newark, New Jersey and a college trustee, made a substantial contribution to be used for the construction of a gymnasium on the campus.

After Scott resigned as president in 1906, he returned to the faculty, spending 16 years teaching political science, constitutional law, international law and civics, in addition to assisting his successor, William H. S. Demarest, with administrative functions.