After the election of 1981 Van Thijn was appointed as Minister of the Interior in the Cabinet Van Agt II, taking office on 11 September 1981. The Cabinet Van Agt II fell just seven months into its term on 12 May 1982 and continued to serve in a demissionary capacity until it was replaced by the caretaker Cabinet Van Agt III on 29 May 1982. After the election of 1982 Van Thijn returned as a Member of the House of Representatives, taking office on 16 September 1982. In May 1983 Van Thijn was nominated as the next Mayor of Amsterdam, he resigned as a Member of the House of Representatives the same day he was installed as Mayor, taking office on 16 June 1983. Van Thijn was appointed again as Minister of the Interior in the Cabinet Lubbers III following the death of Ien Dales, taking office on 18 January 1994. On 27 May 1994 Van Thijn and Minister of Justice Ernst Hirsch Ballin resigned following the conclusions of a parliamentary inquiry report into illegal interrogation techniques used by the police. Van Thijn semi-retired from active politics and became active in the private sector and public sector and occupied numerous seats as a corporate director and nonprofit director on several boards of directors and supervisory boards (Anne Frank Foundation, T.M.C. Asser Instituut, Institute for Multiparty Democracy, Wiardi Beckman Foundation and the Royal Academy of Arts and Sciences) and served as a distinguished professor of Sociology, Governmental Studies and the History of socialism at the University of Amsterdam from 1 December 1995 until 1 December 2003. Van Thijn was elected as a Member of the Senate after the Senate election of 1999, taking office on 8 June 1999 serving as a frontbencher chairing several parliamentary committees. In February 2007 Van Thijn announced his retirement from national politics and that he wouldn't stand for the Senate election of 2007 and continued to serve until the end of the parliamentary term on 12 June 2007.