Bailyn was born in Hartford, Connecticut, the son of Esther (Schloss) and Charles Manuel Bailyn. His family was Jewish. Bailyn earned his bachelor's degree from Williams College in 1945 and in 1953 earned his Ph.D from Harvard University. He was associated with Harvard for the rest of his life. As a graduate student at Harvard, he studied under Perry Miller, Samuel Eliot Morison, and Oscar Handlin. He was made a full professor in 1961, and professor emeritus in 1993. In 1979, he received an honorary doctorate from Grinnell College in Grinnell, Iowa.