Norton was born at Cambridge, Massachusetts. His father, Andrews Norton (1786-1853) was a Unitarian theologian, and Dexter professor of sacred literature at Harvard; his mother was Catherine Eliot, and Charles William Eliot, president of Harvard, was his cousin.

Norton graduated from Harvard in 1846, and started in business with an East Indian trading firm in Boston, travelling to India in 1849. After a tour in Europe, where he was influenced by John Ruskin and pre-Raphaelite painters, he returned to Boston in 1851, and devoted himself to literature and art. He translated Dante's Vita Nuova (1860 and 1867) and the Divina Commedia (1891-91-92), 3 vols.). He worked tirelessly as secretary to the Loyal Publication Society during the Civil War, communicating with newspaper editors across the country, including the journalist Jonathan Baxter Harrison who became a lifelong close friend.. From 1864 to 1868, he edited the highly influential magazine North American Review, in association with James Russell Lowell. In 1861 he and Lowell helped Henry Wadsworth Longfellow in his translation of Dante and in the starting of the informal Dante Club. In 1862 Norton married Susan Sedgwick, creating what for a time became the wealthiest family in Boston.

In 1875 he was appointed professor of the history of art at Harvard, a chair which was created for him and which he held until retirement in 1898. The Archaeological Institute of America chose him as its first president (1879-1890). From 1856 to 1874 Norton spent much time in travel and residence on the continent of Europe and in England, and it was during this period that his friendships began with Thomas Carlyle, John Ruskin, Edward FitzGerald and Leslie Stephen, an intimacy which did much to bring American and English men of letters into close personal relation. Norton had a peculiar genius for friendship, and it is on his personal influence rather than on his literary productions that his claim to fame rests. In 1881 he inaugurated the Dante Society, whose first presidents were Longfellow, Lowell and Norton himself. From 1882 onward he confined himself to the study of Dante, his professorial duties, and the editing and publication of the literary memorials of many of his friends. One of his many students at Harvard was James Loeb, who was later, in 1907, to create The Charles Eliot Norton Memorial Lectureship.

In 1883 came the Letters of Carlyle and Emerson; in 1886, 1887 and 1888, Carlyle's Letters and Reminiscences; in 1894, the Orations and Addresses of George William Curtis and the Letters of Lowell. Norton was also made Ruskin's literary executor, and he wrote various introductions for the American "Brantwood" edition of Ruskin's works. His other publications include Notes of Travel and Study in Italy (1859), and an Historical Study of Church-building in the Middle Ages: Venice, Siena, Florence (1880). He organized exhibitions of the drawings of Turner (1874) and of Ruskin (1879), for which he compiled the catalogues.

During the first years of the twentieth century, Norton spoke out in favor of legalized euthanasia. He lent his name to a movement led by Ohio socialite Anna S. Hall to pass physician-assisted suicide legislation in Ohio and Iowa.

Norton died at "Shady-hill", the house where he had been born, on October 21, 1908, and was buried at Mount Auburn Cemetery. He bequeathed the more valuable portion of his library to Harvard. He had the degrees of Litt.D. (Cambridge) and D.C.L. (Oxford), as well as the L.H.D. of Columbia and the LL.D. of Harvard and of Yale. Today, his name is borne by a series of lectures (Charles Eliot Norton Lectures) held annually by distinguished professors at Harvard.