Flynn was commissioned in the U.S. Army as a second lieutenant in military intelligence in 1981. His military assignments included multiple tours at Fort Bragg, North Carolina, with the 82nd Airborne Division, XVIII Airborne Corps, and Joint Special Operations Command, where he deployed for the invasion of Grenada and Operation Uphold Democracy in Haiti. He also served with the 25th Infantry Division at Schofield Barracks, Hawaii, at the Joint Readiness Training Center at Fort Polk, Louisiana, and the Army Intelligence Center at Fort Huachuca, Arizona.

Flynn served as the assistant chief of staff, G2, XVIII Airborne Corps at Fort Bragg, North Carolina, from June 2001 and the Director of intelligence at the Joint Task Force 180 in Afghanistan until July 2002. He commanded the 111th Military Intelligence Brigade from June 2002 to June 2004 and was the Director of intelligence for Joint Special Operations Command from July 2004 to June 2007, with Service in Afghanistan (Operation Enduring Freedom) and the Iraq War (Operation Iraqi Freedom). He served as the Director of intelligence of the United States Central Command from June 2007 to July 2008, as the Director of intelligence of the Joint Staff from July 2008 to June 2009, then the Director of intelligence of the International Security Assistance Force in Afghanistan from June 2009 to October 2010.

Flynn co-authored a report in January 2010 through the Center for a New American Security, entitled Fixing Intel: A Blueprint for Making Intelligence Relevant in Afghanistan. That report, which became influential, argued that U.S. intelligence agencies "must open their doors to anyone who is willing to exchange information, including Afghans and NGOs (non-governmental organizations) as well as the US military and its allies".

In October 2012, Flynn announced plans to release his paper "VISION2020: Accelerating Change Through Integration", a look at changes he believes are necessary for the DIA in the Future.

Flynn retired from the U.S. Army with 33 years of Service on August 7, 2014.

On December 10, 2015, Flynn attended a gala dinner in Moscow in honor of RT (formerly "Russia Today"), a Russian government-owned English-language media outlet, on which he made semi-regular appearances as an analyst after he retired from U.S. government Service.

Flynn is also an author of The Field of Fight: How We Can Win the Global War Against Radical Islam and Its Allies, co-authored with Michael Ledeen, which was published by St. Martin's Press in 2016. In reviewing the book, Will McCants of the Brookings Institution described Flynn's worldview as a confused combination of neoconservatism (an insistence on destroying what he sees as an alliance of tyranny, dictatorships, and radical Islamist regimes) and realism (support for working with "friendly tyrants"), although he acknowledged that this could be due to the book having two authors.

On December 1, 2017, special counsel Robert Mueller agreed to a plea bargain where Flynn pleaded guilty to "willfully and knowingly" making "false, fictitious and fraudulent statements" to the FBI regarding conversations with Russia's ambassador. Specifically, Flynn is accused of falsely claiming that he had not asked Russia's ambassador to the United States Sergey Kislyak on December 29, 2016, "to refrain from escalating the situation in response to sanctions that the United States had imposed against Russia that same day." Flynn pleaded guilty the same day and acknowledged that he was cooperating with the investigation by Mueller. Flynn stated;

As part of Flynn’s plea negotiations, his son, Michael G. Flynn, is not expected to be charged. As of January 31, 2018, Flynn had not been sentenced.