This son of the minister-professor who was at the center of the 1805 Unitarian Controversy was born in Hingham. He attended Exeter Academy and Harvard College before being voted minister of the Second Church in Boston in 1817.

He married Dr. Benjamin Waterhouse's daughter, Elizabeth. The death of their youngest of three children was followed by his wife's death at the age of thirty. The next year, 1825, Ware was one of the founders of the American Unitarian Association and member of its Executive Committee. When traveling to conduct worship in Northampton, Massachusetts, he experienced a hemorrhage so severe that he was hospitalized in Worcester for six weeks.

Upon recovery of his fragile health, Harvard appointed him professor of pulpit eloquence and pastoral care. Ralph Waldo Emerson, his ministerial colleague at Second Church became his successor as minister. Dr. Ware's pastoral care expressed his devout relation to a personal God and—despite his continuing respect for Emerson—led him to repudiate Emerson's critique of Christianity.

In 1841, when Dr. Ware was in the pulpit of All Souls Church, New York, his pain required him to dismiss the congregation after the hymn before the sermon. After resigning his Harvard chair, he died two years later.