Brinkhorst was elected as a Member of the European Parliament after the European Parliamentary election of 1994, taking office on 19 July 1994. Brinkhorst was appointed as Minister of Agriculture, Nature and Fisheries in the Cabinet Kok II following the resignation of Haijo Apotheker, taking office on 9 June 1999. In February 2002 Brinkhorst announced that he wouldn't stand for the election of 2002. The Cabinet Kok II resigned on 16 April 2002 following the conclusions of the NIOD report into the Srebrenica massacre during the Bosnian War and continued to serve in a demissionary capacity. The Cabinet Kok II was replaced by the Cabinet Balkenende I following the cabinet formation of 2002 on 22 July 2002. Brinkhorst semi-retired from active politics and became active in the private sector and public sector and worked as a senior legal advisor at "NautaDutilh" in Brussels from August 2002 until May 2003 and served as a distinguished professor of Governmental Studies and International relations at the Tilburg University from 1 December 2002 until 27 May 2003.