Flynn met film Actress Marley Shelton on the set of Bubble Boy in 2000, and the two married in July 2001. Their first daughter, West Flynn, was born on September 6, 2009. Ruby Jeanne Flynn, their second daughter, was born on May 1, 2012.
On August 22, 2011, after starting his company, Flynn Picture Company, Flynn again signed on with the New Line for a two-year first-look deal. He agreed to continue to produce big concept studio films. FlynnPictureCo's staff includes Senior Vice President Wendy Jacobson, Vice President Scott Sheldon, Assistant to Beau Flynn Shelby Thomas and Assistant to Wendy Jacobson and Scott Sheldon Sawyer Bock.
On May 29, 2013, 20th Century Fox acquired Ben Mezrich's book Seven Wonders for a trilogy. Flynn and Brett Ratner produced the film through their different companies. On June 5, 2013, Universal Pictures acquired the remake rights to the 2007 anime Vexille which Flynn would be producing along with Vinson. On September 19, 2014, New Line set Flynn to produce the crime thriller North of Reno written by Banipal and Benhur Ablakhad.
Flynn’s San Andreas, stars Dwayne Johnson and Carla Gugino and is directed by Brad Peyton. The 3D disaster film, written by Carlton Cuse, is based on Flynn’s original idea and was released by Warner Bros. worldwide on May 29, 2015.
