Benjamin Cluff Jr. was born in Provo, Utah on February 7, 1958 to Benjamin Cluff and Mary Ellen Foster. In 1877, Cluff enrolled in Brigham Young Academy and began working as a janitor to pay for his tuition. However, soon after he received a call to serve a mission to the Sandwich Islands. Returning to Utah in 1882, Cluff was offered a teaching job as an instructor of mathematics at Brigham Young Academy by Karl G. Maeser. In 1886, he attended the University of Michigan and received his bachelor of science in 1890. Upon his return to Utah, he became the assistant principal of the Brigham Young Academy.

Cluff was married to Mary Jane John in 1883, and later entered into marriage with Harriet Cullimore in 1886, and Florence Mary Reynolds in 1898. He had twenty-one children with his three wives.

Under Cluff's direction, plans for a new building were begun and students selected white and blue as the school colors. Cluff returned to the University of Michigan for a master's degree in 1893, and became the principal of Brigham Young Academy when he returned to Utah. In 1895, Cluff's title was changed to president, and heads of departments were named principals. He led an expedition of students to South America in 1900 for the purpose of archaeological research. On October 3, 1903, the school became Brigham Young University. In December, Cluff resigned and took a position as superintendent of a rubber plantation in Mexico. The Cluffs returned to the United States in 1924 and opened a store in Southern California. Cluff died June 14, 1948, in Redondo Beach, California.