In 1997, he moved to Yale University to become the Lovett Professor of Military and Naval History. In the 2000–01 academic year, Gaddis was the George Eastman Professor at Oxford, the second scholar (after Robin Winks) to have the honor of being both Eastman and Harmsworth professor. In 2005, he received the National Humanities Medal. He sits on the advisory committee of the Wilson Center's Cold War International History Project, which he helped establish in 1991. Gaddis is also known for his close relationship with the late George Kennan and his wife, whom Gaddis described as "my companions".
Gaddis is probably the best known historian writing in English about the Cold War. Perhaps his most famous work is the highly influential Strategies of Containment (1982; rev. 2005), which analyzes in detail the theory and practice of containment that was employed against the Soviet Union by Cold War American presidents, but his 1983 distillation of post-revisionist scholarship similarly became a major channel for guiding subsequent Cold War research.
We Now Know (1997) presented an analysis of the Cold War through to the Cuban Missile Crisis that incorporated new archival evidence from the Soviet bloc. Fellow historian Melvyn Leffler named it as "likely to set the parameters for a whole new generation of scholarship". It was also praised as "the first coherent and sustained attempt to write the Cold War's history since it ended." Nonetheless, Leffler observed that the most distinctive feature of We Now Know is the extent to which Gaddis "abandons post-revisionism and returns to a more traditional interpretation of the Cold War." 
The Cold War (2005), praised by John Ikenberry as a "beautifully written panoramic view of the Cold War, full of illuminations and shrewd judgments," was described as an examination of the history and effects of the Cold War in a more removed context than had been previously possible, and won Gaddis the 2006 Harry S. Truman Book Prize. Critics were less impressed, with Tony Judt summarising the book as "a history of America's cold war: as seen from America, as experienced in America, and told in a way most agreeable to many American readers," and David S. Painter writing that it was a "carefully crafted defense of US policy and policymakers" that was "not comprehensive." 
John Nagl, in the Wall Street Journal, wrote of Gaddis's 2018 book On Grand Strategy as "a book that should be read by every American leader or would-be leader".
Gaddis is known for arguing that Soviet leader Joseph Stalin's personality and role in history constituted one of the most important causes of the Cold War. Within the field of U.S. diplomatic history, he was originally most associated with the concept of post-revisionism, the idea of moving past the revisionist and orthodox interpretations of the origins of the Cold War to embrace what were (in the 1970s) interpretations based upon the then-growing availability of government documents from the United States, Great Britain and other western government archives. Due to his growing focus on Stalin and leanings toward US nationalism, Gaddis is now widely seen as more orthodox than post-revisionist. The revisionist Bruce Cumings had a high profile debate with Gaddis in the 1990s, where Cumings criticized Gaddis as moralistic and lacking in objectivity.
Gaddis is close to President George W. Bush, making suggestions to his speech writers, and has been described as an "overt admirer" of the 43rd President. After leaving office, Bush took up painting as a hobby at Gaddis's recommendation.
During the US invasion of Iraq, Gaddis argued: “The world now must be made safe for democracy, and this is no longer just an idealistic issue; it’s an issue of our own safety.”  During the United States occupation of Iraq, Gaddis asserted that Bush had established America “as a more powerful and purposeful actor within the international system than it had been on September 11, 2001.” Historian James Chace argues that Gaddis supports an "informal imperial policy abroad."  Gaddis believes that preventive war is a constructive part of American tradition, and that there is no meaningful difference between preventive and pre-emptive war.
"You can't gobble all your treats on Halloween without throwing up." 
Gaddis, John Lewis (1990). "New Conceptual Approaches to the Study of American Foreign Relations: Interdisciplinary Perspectives". Diplomatic History. 14 (3): 405–424. doi:10.1111/j.1467-7709.1990.tb00098.x.