In 1878 he published his first volume of sermons, and from time to time issued other volumes, including Sermons Preached in English Churches (1883) and "The Candle of the Lord" and Other Sermons (1895).
Today, he is probably best known for authoring the Christmas carol "O Little Town of Bethlehem".
Brooks wrote that his only ambition was "to be a parish priest and, though not much of one, [I] would as a college president be still less".
Under his inspiration, architect Henry Hobson Richardson, muralist John La Farge, and stained glass artists William Morris and Edward Burne-Jones created an architectural masterpiece in Trinity Church, Boston, among the notable features of which was the first freestanding liturgical altar in the United States in an overall chancel design that attracted attention for its Liturgical Movement influence even in British architectural magazines.
His sermon at Harvard's commemoration of the Civil War dead in 1865 likewise attracted attention nationwide.
In 1869 he became rector of Trinity Church, Boston; today, his statue is located on the left exterior of the church.
Although he despaired of Anglo-Catholic ritualism, he championed many aspects of the liturgical movement including congregational singing at the liturgy.
At the eucharist, for instance, he would preach, not from the pulpit, but from the chancel steps, and although he liked to preach in a black academic gown he never failed to appear in a comodious white surplice and priest's stole when he officiated at the office or eucharist.
During the American Civil War he upheld the cause of the North and opposed slavery, and his sermon on the death of Abraham Lincoln was an eloquent expression of the character of both men.
John Cotton; through his mother, Mary Ann Phillips, he was a great-grandson of Samuel Phillips, Jr., founder of Phillips Academy (Andover, Massachusetts).
Three of Brooks' five brothers – Frederic, Arthur and John Cotton – were eventually ordained in the Episcopal Church. He worked briefly as a school teacher at Boston Latin, but, upon being fired, felt that he had failed miserably.
His death was a major event in the history of Boston.
One observer reported: "They buried him like a king.On April 30, 1891 he was elected sixth Bishop of Massachusetts, and on the 14 October was consecrated to that office in Trinity Church.