Harkness was born in Mendon, Massachusetts[1] and attended Uxbridge High School and Worcester Academy.

[3] He was senior master of Providence High School from 1846 to 1853,[4] and pursued studies in Germany at the universities of Berlin, Bonn, and Göttingen.

[6] He visited Europe in 1870 and 1883 and there investigated educational questions, in particular the methods of German and English universities.

[10] He lectured extensively before learned societies, contributed valuable papers on original researches in philology to the Transactions of the American Philological Association, and from 1851 published a series of textbooks in Latin studies, of which it may be said that from them dated the beginning of a new era in the Latin department of classical studies in America.

Their son Albert Granger Harkness was a Professor of Roman Literature and History at Brown University,[13] and their daughter Clara Frances married William Carey Poland, a professor at Brown University.