Jesper Juul was born in Vordingborg, Denmark. He had several jobs before entering higher education at Marselisborg Seminarium 1966-1970 where he graduated as a teacher of history and religion. He then enrolled in studies of the history of ideas at the University of Aarhus. He financed his studies working at family resort Bøgholt in Viby J, and dropped out of studies to work full time with social treatment. At an internal course he became acquainted with U.S. psychiatrist Walter Kempler and they became friends, finally leading to him forming the Kempler Institute of Scandinavia in 1979 with Kempler as a director. A few years later Juul had to take over leadership of the institute and would hold this position until 2004.

In his first marriage 1971-1990 he has one son, Nicolai, and his second marriage in 1991 with Suzana, a woman from former Yugoslavia, has resulted in him working on a voluntary basis with refugees and war veterans in Bosnian and Croatian locations about three months a year, also providing leadership and organizational development for non-governmental organizations.