Becker studied at the University of Wisconsin (B.A., 1896; Ph.D., 1907) and Columbia University. He taught at the University of Kansas, Lawrence, from 1902 to 1916 and at Cornell University, Ithaca, N.Y., from 1917 until he retired in 1941. In The Beginnings of the American People (1915), he elaborated on his doctoral work by advancing the thesis of a dual American Revolution—the first being the struggle for self-government and the second the ideological battle over the form such government should take. In The Eve of the Revolution (1918) and The Declaration of Independence (1922), he further probed the relationship between 18th-century natural-rights philosophy and the American Revolution.

The interwar period was a time of dejection and increasing philosophical skepticism for Becker. During the 1920s, particularly, he began challenging the then-orthodox assumption of the superiority of a scientific methodology in historical study. He maintained that perceived “facts” are basically mental images created by the historian's experience and a larger, socially defined reality that determines the process by which the historian selects his data. His presidential address in 1931 to the American Historical Association, “Everyman His Own Historian” (published in 1932 and expanded to book length in 1935), deals most explicitly with this theme of historical relativism. In one of his best-known books, The Heavenly City of the Eighteenth Century Philosophers (philosophe) (1932), Becker not only examined the ideas of the Philosophes, such as their belief in progress and human perfectibility, but also stressed their intellectual fervour and their success in bridging traditional Christianity and Enlightenment secularism. During World War II he repudiated his earlier skepticism, urging the need for a reinsertion of moral statements in historical writing.