He was educated at the City of London School and at St John's College, Cambridge, where he took the highest honours in classics, mathematics and theology, and became fellow of his college. In 1862 he took orders. After holding masterships at King Edward's School, Birmingham, and at Clifton College, he succeeded G. F. Mortimer as headmaster of the City of London School in 1865 at the early age of twenty-six. He was Hulsean lecturer in 1876.
He retired in 1889, and devoted himself to literary and theological pursuits. Dr. Abbott's liberal inclinations in theology were prominent both in his educational views and in his books. His Shakespearian Grammar (1870) is a permanent contribution to English philology. In 1885 he published a life of Francis Bacon. His theological writings include three anonymously published religious romances - Philochristus (1878), Onesimus (1882), and Sitanus (1906).
More weighty contributions are the anonymous theological discussion The Kernel and the Husk (1886), Philomythus (1891), his book The Anglican Career of Cardinal Newman (1892), and his article "The Gospels" in the ninth edition of the Encyclopędia Britannica, embodying a critical view which caused considerable stir in the English theological world. He also wrote St Thomas of Canterbury, his Death and Miracles (1898), Johannine Vocabulary (1905), Johannine Grammar (1906). Flatland was published in 1884.
His brother, Evelyn Abbott (1843 - 1901), was a well-known tutor of Balliol College, Oxford, and author of a scholarly history of Greece.