Duncan Hunter has served as the chairman of the House Armed Services Committee since 2002. From there, he has made some micromanaging decisions regarding women in the military and intelligence funding, as well as military spending. He has stated that in his view, our government's "highest obligation is owed to our forces in uniform, especially during this time of war.", and has been critical of colleagues and measures which fall short of this mark. He has also been an outspoken advocate of aerospace defense funding, calling on the Department of Defense to expedite actions to test and adopt new defensive weapons.

In 2005, he introduced the Right to Life Act, a move against abortion rights. He introduced the Parents Empowerment Act in 2004, which would empower parents and guardians to sue any individual who exposes their charge to pornography. He also mandated more border security fencing between San Diego County and Tijuana; this legislation was later included with the Secure Fence Act.

He has actively opposed international trade agreements such as NAFTA, CAFTA and the WTO.

He has also created the Peace Through Strength political action committee, which advocates that international peace is only possible through military strength, much similar to how foreign policy was under the Cold War.

In 2006, Duncan Hunter announced his candidacy to run for the office of United States President in 2008. His campaign has gotten off to a rather ragged run, however, but there may be a second possible office in his future, as another candidate, Mike Huckabee, has mentioned that Hunter would be good to fill in a position as Secretary of Defense in his cabinet.

Duncan Hunter is a political curiosity. While remaining a very central Conservative Republican, he has consistently kept in touch with a Democratic voting base in his district and has won support from both sides of the party fence in ways that almost cannot be explained. Part of it may be his working-class roots and his military service. He can count on the votes from the military and defense contract base, as well as the wealthy industries around the perimeter of the military.