Born in Warwickshire, England, he was a son of William and Catharine (née Sidwell) Johnson. His father was an English Methodist preacher. Bishop Johnson was also descended from one of John Wesley's helpers. Eben married Sarah Tilsley, with whom he had children Damuel D., Arthur H., and Dorothea.
Eben then emigrated to the United States of America, where he earned both the A.B. and the A.M. degrees from Morningside College. Syracuse University later awarded him the honorary degree Doctor of Divinity.
The Rev. Eben Samuel Johnson actually preached on an English circuit at the age of sixteen! In America he entered the Northwest Iowa Annual Conference in 1889. As a Pastor he served the following appointments: Danbury, Wall Lake, Mapleton, Sac City, Webster City, and Rock Rapids. He then was appointed Superintendent of the Ida Grove District. In 1909 he was appointed Pastor of the First Methodist Church, Sioux City, where his address was 514 7th St., Sioux City.
He served his Annual Conference as the Secretary, then the Chairman of the Examining Board; as the President of the Conference Board of Education; and as a Members of M.E. General Conferences, 1904-16. He served as General Conference Journal Secretary for a time, as well. He also was a Trustee of Morningside College.
During the Spanish-American War, the Rev. Johnson served as a Chaplain in the 52nd Iowa Infantry Regiment, U.S. Voluteers. He also served in the 56th Regiment of the Iowa National Guard, first with the rank of Captain, then Major (United States).
Bishop Johnson died at the Veterans' Hospital in Portland, Oregon. He was buried in Riverview Abbey in Portland.