Benjamin Cluff, Jr. was born in Provo, Utah on February 7, 1858. He spent his early years in Logan, Utah. At age seven, he went with his family to Hawaii where his father was serving as a missionary for the Church of Jesus Christ of Latter-day Saints. After five years, he returned to Logan and, in 1877, attended the newly founded Brigham Young Academy in Provo, Utah, remaining there until 1886 except for serving his own mission to Hawaii from 1878 to 1882. In 1886, he traveled to Ann Arbor, Michigan to study at the university there. He completed his master's degree there in 1894 and was one of the first Mormons to graduate from an eastern university.

He became the president of the Brigham Young Academy in 1892 upon the retirement of Karl G. Maeser. Under his direction as president, white and blue were selected as the school colors; class organizations were inaugurated; Founder's Day was instituted; a student loan association was organized; the first summer school was started; the Alumni Association was founded; and the first non-Mormon faculty member was hired. At Cluff's recommendation, the name of the school was changed to Brigham Young University in 1903.

In 1900, Cluff led an expedition of students and faculty to Central America, hoping to both upgrade the museum and scientific work of the academy as well as place serious learning on a firmer foundation at the school. He resigned from the presidency in 1903, and accepted a job managing a plantation in Tabasco, Mexico. After many years there, he moved to southern California and went into business for himself. He died June 16, 1948.