Fallon commanded Attack Squadron 65, embarked in USS Dwight D. Eisenhower; Medium Attack Wing One at NAS Oceana; and Carrier Air Wing Eight aboard USS Theodore Roosevelt during a combat deployment to the Persian Gulf for Operation Desert Storm in 1991.

He has served as Deputy Director for Operations, Joint Task Force Southwest Asia (JTF-SWA) in Riyadh, Saudi Arabia, and as Deputy Director, Aviation Plans and Requirements on the Staff of the Chief of Naval Operations in Washington, D.C. His first flag officer assignment was with NATO as Assistant Chief of Staff, Plans and Policy for Supreme Allied Commander, Atlantic.

In February 2001, while serving as Vice Chief of Naval Operations, Fallon was given Presidential special envoy status and dispatched to Japan to apologize for the collision between the U.S. Navy submarine USS Greeneville and the Japanese fisheries training vessel Ehime Maru.

Fallon, along with Ambassador Tom Foley, met with family members of the victims at the Ambassador's official residence in Tokyo and in the Ehime Maru's home port of Uwajima, Ehime Prefecture, bowing deeply and expressing regret on behalf of the United States and President George W.

[6] His deferential show of contrition to the families, carried out in front of news cameras, was widely credited with defusing an incident that could have damaged U.S.-Japan relations.

[13] In an Al-Jazeera broadcast on 30 September 2007, he criticized those publicly urging war, stating "This constant drum beat of conflict is what strikes me which is not helpful and not useful.

[18][19] After his widely publicized resignation, interpreted as opposition to military action against Iran, the conservative The Washington Times countered with a report that Fallon's active and retired military critics believed that he was "pushed to resign" by higher officials because "he failed to prevent foreign fighters and munitions from entering Iraq".

[20] Fallon joined the Massachusetts Institute of Technology (MIT) Center for International Studies as a Robert Wilhelm Fellow for nine months, starting August 2008.

[4] He also was the 2009 commencement speaker for the University of California, San Diego's Graduate School of International Relations and Pacific Studies.

[22] Starting in June 2009, Admiral Fallon served as co-chair of the Center for Strategic & International Studies Commission on Smart Global Health Policy[23] alongside the President and CEO of CARE, Helene D. Gayle where he discussed his experiences with the security dimensions of global health.

Admiral Fallon contributed in multiple conferences and policy discussions and attended a summer tour of Kenya that included the Kibera slums.

Admiral Fallon joined Tilwell Petroleum LLC in August, 2009 as a partner and advisor for the company's strategic business development program.

"Admiral Fallon's extensive experience in the Navy and his work with government and non-governmental agencies is a great addition to Tilwell as we continue to expand our customer base and support for both military and commercial applications.