Flynn was one of seven children born to Terry and Kathleen Flynn, and a graduate of Saint Thomas Academy (1984) and the University of St. Thomas (1989).
Post graduation, Flynn went to work for Kraft Foods as an account and sales marketing specialist. In 1991, he left Kraft to pursue a career as an aviator with the United States Marine Corps. One week before leaving for Officer Candidate School, he was medically disqualified from the Marine Aviation Program. In an effort to overcome the difficulties of dyslexia, Flynn forced himself into a daily writing and reading regimen. His writing influences included Clancy, Hemingway, Irving, Ludlum, Tolkien, and Vidal.
His newfound interest in such novels motivated him to begin work on a novel of his own. While employed as a bartender in the St. Paul area, he completed his first book, Term Limits, which he then self-published.
"I had just finished reading The Government Racket: Washington Waste from A to Z, by Martin L. Gross. It is without a doubt the most disheartening and enlightening book about politics that I've ever read. I was out jogging one day wondering what it would take to really change Washington, when my thoughts turned to a friend who had been shot and killed in Washington, D.C., several summers earlier. As I continued running, a story started to unfold."
Pocket Books published the hardcover edition of Term Limits in 1998, and the mass market paperback of Term Limits in 1999, which spent several weeks on The New York Times bestseller list. Subsequent works, including Flynn's 1999 novel, Transfer of Power, his 2000 novel The Third Option and his 2001 novel Separation of Power, also appeared on the New York Times bestseller list, with Separation of Power reaching as high as #7.
Flynn's fifth novel, Executive Power, was published in hardcover by Atria Books in May 2003, followed by his sixth novel, Memorial Day in 2004, his seventh novel Consent To Kill in October 2005, his eighth novel Act Of Treason in October 2006, his ninth novel Protect And Defend in 2007 and his tenth novel Extreme Measures in 2008. With the exception of his first novel Term Limits, his works centered around counter-terrorism agent Mitch Rapp. His 2008 release, Extreme Measures, became the ninth novel in the series.
Flynn wrote six New York Times bestsellers for Atria Books, and had a contract for four more. He remembered deciding between following the path that was the most uncomfortable—continuing with what looked to be a promising career as a commercial real estate leasing agent—or taking a big risk and start a new career as a writer: "I look back on it now and I couldn't be happier with my decision, but at the time I remember a lot of people thought I was nuts."
In February 2008, Flynn agreed on film and book projects with CBS Corporation units CBS Films and Simon & Schuster/Atria Books. Lorenzo di Bonaventura was negotiating to produce Mitch Rapp films. The first film, American Assassin, was released on September 15, 2017. Atria Books got worldwide rights to four books by the author. In August 2010, Flynn signed a two-book deal for a new series that he would have co-written with Brian Haig, a retired Army Lieutenant Colonel. He was a frequent guest on The Glenn Beck Radio Program on the Fox News Channel, and on Dan Barreiro's radio program on Twin Cities station KFAN.
Flynn lived with his wife, Lysa, and their three children in the Twin Cities (Minneapolis-St. Paul) area.
On February 1, 2011, in his fan newsletter, Flynn announced that he was being treated for advanced Stage III prostate cancer. He died of a rare form of aggressive prostate cancer in Saint Paul, aged 47, on June 19, 2013, at 1:15 a.m., surrounded by family and friends.