Meditations on the Five Joyful Mysteries, together with a Letter Dedicatory to the Mother Superior of the Sisters of S. Mary.
New York: J. Pott & Co., 1888.

The Man and the Movement. A Monograph upon the Life and Work of John Henry Newman so far as These Relate to the Catholic Movement in the Church of the English
New York: J. Pott & co., 1890.

A Voice in the Wilderness: Being a Plea for the Restoration of Primitive Christianity Addressed to the Bishops of the Anglo-American Communion and through them to the English-speaking People throughout the World.
New York: J. Potts, 1897.

The Story of a Simple Life: Being an Account of the Life and Labors of Sarah Wisner Thorne.
New York: T. Whittaker, 1900.

Political Crimes and Their Consequences
By Algernon Sidney Crapsey
No place: no publisher, [1901].

A Constitutional Defense of the Negro
By Algernon Sidney Crapsey, Delivered at a Mass Meeting of Citizens in the Metropolitan A.M.E. Church, Washington, D.C., December 15, 1901.

Prison Methods.
New York: Prison Association of New York, 1902.

Passive Resistance: Jesus' Method of Government
Boston: American Peace Society, 1905.

Religion and Politics
New York: T. Whittaker, 1905.

Proceedings upon the Trial of Rev. Dr. A.S. Crapsey for Heresy.
New York: Thomas Whittaker, 1906.

Appeal by the Rev'd Algernon S. Crapsey, S.T.D. to the Court of Review of the Protestant Episcopal Church
New York: Thomas Whittaker, 1906.

For the Church Living and Universal. Argument of Edward M. Shepard as Counsel for the Rev. Algernon S. Crapsey, S.T.D., before the Court of Review of the Protestant Episcopal church, upon his Appeal from the Judgment of the Court of the Diocese of Western New York.
By Edward Morse Shepard
No place: no publisher, 1906.

The Re-birth of Religion: Being an Account of the Passing of the Old and Coming of the New Dogmatic
New York: John lane, 1907.

The Rise of the Working-class
New York: The Century Co., 1914.

International Republicanism, the Way to Permanent Peace.
Philadelphia: Society for Ethical Culture, 1918.

The Ways of the Gods
New York: International Press, 1921.

The Last of the Heretics
New York: A.A. Knopf, no date, but 1924.