On 6 September 1988 Van Eekelen resigned following the conclusions of a parliamentary inquiry report into a passport fraud investigation that was mishandled by him during the time he serves as State Secretary for Foreign Affairs in the previous cabinet, his successor as State Secretary for Foreign Affairs René van der Linden subsequently resigned on 9 September 1988.

Van Eekelen remained active in national politics, in April 1989 he was nominated as Secretary General of the Western European Union, serving from 15 May 1989 until 15 November 1994.

In January 2003 Van Eekelen announced his retirement from national politics and that he wouldn't stand for the Senate election of 2003 and continued to serve until the end of the parliamentary term on 10 June 2003.

Van Eekelen retired after spending 26 years in national 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 (Institute for Multiparty Democracy, Achmea, Netherlands Atlantic Association, Transnational Institute, Carnegie Foundation and the Institute of International Relations Clingendael) and served as a diplomat and lobbyist for several economic delegations on behalf of the government and as an advocate and lobbyist for Democracy, NATO and European integration.

Van Eekelen continues to comment on political affairs as of 2025 and holds the distinction as the only Dutchman that served as Secretary General of the Western European Union.