De Hoop Scheffer continued to be active in politics and was appointed as Minister of Foreign Affairs in the Balkenende I cabinet taking office on 22 July 2002.

De Hoop Scheffer retired from active politics at 61 and became active in the private and public sectors as a corporate and non-profit director served on several state commissions and councils and as a occasional diplomat and lobbyist for several economic delegations on behalf of the government, he also worked as a distinguished professor of International relations, Diplomatic Practice and Governmental Studies at his alma mater Leiden University from September 2009 until September 2014.

De Hoop Scheffer was granted the honorary title of Minister of State on 22 June 2018 and as of 2025 continues to comment on political affairs as a statesman.

Its main foreign policy decision was to contribute to Operation Iraqi Freedom, although its formulation ("political" but not "military" support) gave it an ambivalent character.

However, 1,100 Dutch servicemen were deployed as part of the Stabilisation Force Iraq in the southern province of Al Muthanna from 2003 till 2005, and two of them were killed in action.

[4] He "informed a NATO conference that 'NATO troops have to guard pipelines that transport oil and gas that is directed for the West,' and more generally to protect sea routes used by tankers and other 'crucial infrastructure' of the energy system".

[5] On 21 June 2007, De Hoop Scheffer attended an economic conference in Montreal where he encouraged Canada to continue its military mission in Afghanistan past its 2009 withdrawal date.

"[7] De Hoop Scheffer's comments were made as the Harper government was under pressure by opposition politicians to define the length of Canada's commitment to the mission in Afghanistan.

It has been alleged by Iran that Jaap de Hoop Scheffer met Jundallah leader Abdolmalek Rigi while he was visiting Afghanistan in 2008 amid Iranian accusations that the CIA was backing the terrorist group.