* The Beginnings of Christianity (1879) - A comprehensive study of the origins and development of Christianity in the first century.
* The History of the Christian Church (1887) - A comprehensive account of the history of the Christian Church from its beginnings to the Reformation.
* The Reformation (1873) - A detailed account of the Protestant Reformation in Europe.
* The Grounds of Theistic and Christian Belief (1885) - A defense of Christianity and its core beliefs.
* The Nature and Method of Revelation (1860) - A philosophical exploration of the nature of revelation.
Fisher also wrote several biographies, including:
* The Life of Benjamin Silliman (1866) - A biography of the renowned American scientist.
* The Life of James Monroe (1883) - A biography of the fifth President of the United States.
His works were highly influential in their time and continue to be studied by scholars of history and theology.