On 1 April 2000, Lim succeeded Bey Soo Khiang as Chief of Defence Force, and was promoted from Major-General to Lieutenant-General in June 2001.

[1][2] Lim retired from the SAF on 1 April 2003 and was succeeded by Ng Yat Chung as Chief of Defence Force.

[3] After leaving the Singapore Armed Forces (SAF), Lim served as Permanent Secretary for Education (MOE) between 2003 and 2007.

[2] Lim served as Chairman of the Agency for Science, Technology and Research (A*STAR), a statutory board under the Ministry of Trade and Industry, between 2007 and 2019.

Lim is also a member of various other organisations; NTU, Biomedical Research Council at A*STAR, National Research Foundation, Science and Technology in Society (STS) [ja], and the World Premier International Initiative Programme Assessment and Review Committee in Japan.