Hafen was born in Scherzingen, Switzerland. His parents joined The Church of Jesus Christ of Latter-day Saints (LDS Church) and immigrated to Utah Territory. When they first came to Utah, the family lived in Payson. In 1868, Hafen began attending the 20th Ward Academy in Salt Lake City, where one of the main teachers was Karl G. Maeser. Hafen learned painting from George Ottinger and Dan Weggeland.
Hafen was one of the founders of the Utah Art Association in 1881.
In 1890, Hafen, Lorus Pratt and John B. Fairbanks were sent as art missionaries to Paris, where they studied at the Académie Julian under Albert Rigolot. At this point he left his wife, Thora Twede Hafen, and their five children in Springville, Utah. After they completed their studies, the Mormon artists returned to Utah and created murals in the Salt Lake Temple.
After returning from France, Hafen's main focus was on landscape painting. He donated paintings to Springville that were the initial basis of the Springville Art Museum. Hafen had five more children with his wife, the youngest being born in 1904.
Hafen was a professor at Brigham Young Academy, where he developed the art department. He was recruited to come there to do this specifically by Benjamin Cluff. Hafen lived in Springville, in a home designed by Alberto O. Treganza. The house is listed on the U.S. National Register of Historic Places as the John Hafen House.
- Conant 1969, pp. 5, 39
- American Art Annual, Volume 8. MacMillan Company. 1911. p. 398.
- Brian Q. Cannon. "Shaping BYU: The Administration and Legacy of Benjamin Cluff, Jr" in BYU Studies Vol. 48, no. 2, p. 17
- Karl Haglund and Kirthy Ann Luney (July 1980). "National Register of Historic Places Inventory/Nomination: John Hafen House". National Park Service. and accompanying photos
- Utah Artists Project bio of Hafen
- Conant, William Lee Roy, Jr. (August 1969), A Study of the Life of John Hafen, Artist (Master's thesis), Provo, Utah: Department of Art, Brigham Young University.
- Todd, Jay M. (August 1976), John Hafen, Ensign: 60.
- Oman, Richard G. (1992), "Artists, Visual", in Ludlow, Daniel H, Encyclopedia of Mormonism, New York: Macmillan Publishing, pp. 70–73, ISBN 0-02-879602-0, OCLC 24502140