He was serving as Deputy Prime Minister alongside Tony Tan and Wong Kan Seng.

During the 1991 general election, he remained as the MP for the Bedok constituency but this time under the newly created East Coast GRC.

On 1 September 2005, Jayakumar took over the role as Coordinating Minister for National Security from Tony Tan to oversee counter-terrorism policies in Singapore.

He also resigned as a permanent member of the Presidential Council for Minority Rights which he was appointed to the position on 1 July 1998.

[14] In the investiture ceremony, he was praised for having "given his entire life to the service of Singapore" and the citation of his award said: "Uniquely among public servants, Prof Jayakumar brought an exceptionally keen legal mind to bear on a considerable range of issues, from national security and foreign policy to political and constitutional developments.

"[14] Jayakumar has written and published several books related to his life and experiences in foreign affairs and diplomacy.

In 2009, Jayakumar and Ambassador-at-Large Tommy Koh published the book titled Pedra Branca: The Road to the World Court, which covers the territorial dispute between Malaysia and Singapore over Pedra Branca, a small island of strategic value located near the entry point to the Straits of Malacca.

[19] In November 2020, Jayakumar introduced his book titled Governing: A Singapore Perspective, which covers his views and experiences of Singapore's governance, such as how he viewed the Lee family dispute over their 38 Oxley Road home, and Prime Minister Lee Hsien Loong's retirement plan if the COVID-19 crisis has not improved.