Borghouts was born in Ginneken on 17 June 1939. He obtained his doctorate at Leiden University in 1971 with a dissertation titled: The magical texts of Papyrus Leiden I 348. From 1969 to 1976 he worked as a scientific employee at the Egyptological Seminar of the University of Amsterdam. He returned to Leiden University in 1976.
Borghouts succeeded Jac. J. Janssen as professor and head of the Egyptology department in 1985. Under Borghouts the department reached its maximum size. Around the year 2000 the department became threatened by budget cuts. Borghouts defended the needs of the department and stated that he would see the department become academically irrelevant otherwise. Borghouts retired in 2004. However, he remained attached to Leiden University and The Netherlands Institute for the Near East.
- "Joris Frans Borghouts" (in Dutch). Leiden University. Retrieved 4 January 2017.
- O.E. Kaper & O.G. Dercksen (2014). "Waar de geschiedenis begon: Nederlandse onderzoekers in de ban van spijkerschrift, hiërogliefen en aardewerk". Netherlands Institute for the Near East. pp. 46–51. Retrieved 4 January 2017.
- "Kleine Letteren voelen zich bedreigd" (in Dutch). Mare Online. 2001. Retrieved 4 January 2017.
- "Bijna de mond gesnoerd" (in Dutch). de Volkskrant. 12 May 2001. Retrieved 4 January 2017.
- "Prof. dr. J.F. (Joris) Borghouts (Emeritus)". Leiden University. Retrieved 4 January 2017.
- "J.F. Borghouts". Royal Netherlands Academy of Arts and Sciences. Archived from the original on 4 January 2017.
- "In Memoriam Prof. Dr. J.F. Borghouts". NINO Leiden. Archived from the original on 29 March 2019. Retrieved 24 September 2018.