He opened up youth camps in the United States, and was youth coach in various countries, coaching at Lebanese football clubs, Dutch clubs, AFC Ajax, VV Venray and Al Ain FC.
In 1999, he was employed by AFC Ajax as the manager of the international youth system, working with the academies in Ghana, Belgium and South Africa.
In 2008, he succeeded Hans Vonk as the technical director at Ajax Cape Town.
In late 2012, Jan Pruijn occupied another interim coaching position at Ajax CT, succeeding Wilfred Mugeyi's interim position, following the dismissal of Maarten Stekelenburg as coach of Ajax Cape Town.
He was relieved by Jan Versleijen who took over as interim coach, before resigning prematurely, and Muhsin Ertuğral finishing the season with Ajax CT after being appointed Technical director of the Cape club.