Shortly before his birth, his parents had recently moved to Boston from Duxbury, Massachusetts, where the Winsor family had been involved in shipbuilding for generations.

His grandfather's home, the Nathaniel Winsor, Jr. House, is now the headquarters of the Duxbury Rural and Historical Society.

Justin Winsor published his first book, A History of the Town of Duxbury (1849), during his first year at Harvard.

As a member of the Boston Brahmins, Winsor found an opportunity to engage in social reform while pursuing intellectual interests.

They espoused the Socratic idea that knowledge creates virtue and Winsor saw the public library as a way to educate common people so that the traditional order of the republic would be maintained.

He also dedicated a great deal of attention to the compilation of bibliographies and guides to public reading.

In an effort to increase book use, he worked for the establishment of branch libraries, extended hours, and relaxed restrictions on use.

In this effort, he pushed for more books and greater accessibility, improved the catalog, informed faculty of new acquisitions, liberalized the library use policy, instituted a reserve system, and wrangled with administration over the installation of electric lights for extended hours.

[3] Winsor was a founding member of the American Historical Association and served as their third president during the 1886–1887 term.

Following illness over a period of time, Winsor dealt with a strangulated hernia while staying at his home in Cambridge, Massachusetts.