Byrnes grew up in Washington, D.C., where he attended and played second base for St. Albans School. He graduated in 1992 from Haverford College with a BA in English. He played on the collegiate baseball team while attending Haverford. He began his professional career with a health-care consulting company after school. He began his baseball career for the Cleveland Indians in 1994, quickly working his way up the organizational ladder, first as an intern, then as a video scout, and, eventually, to the position of scouting director in 1998. In 1999, he was hired by colleague Dan O'Dowd to fill the assistant GM position for the Colorado Rockies, a job he held for two years. He then took the same job under Theo Epstein and the Boston Red Sox until October 2005, when he was hired by the Diamondbacks to replace the departing interim General Manager Bob Gebhard.
Part of the new breed of young general managers, Byrnes was 35 when he was hired by the Diamondbacks in 2005. In February 2008, he was given an 8-year extension that was to last through the 2015 season.
With the Diamondbacks in last place, 12.5 games of first-place San Diego, and citing a need for accountability and overall change, owner Ken Kendrick and team President Derrick Hall announced on July 2, 2010 that both Josh Byrnes and team manager A.J. Hinch had been relieved of their duties. Josh Byrnes was replaced on an interim basis by Jerry DiPoto and Hinch was replaced also on an interim basis by bench coach Kirk Gibson.
On December 3, 2010, Byrnes was hired by the San Diego Padres as their Vice President of Baseball Operations, reuniting him with GM Jed Hoyer, with whom he worked in Boston, and team owner Jeff Moorad, who was the previous CEO of the Diamondbacks.
On October 26, 2011, Josh Byrnes was promoted to General Manager of the San Diego Padres. On June 22, 2014 Byrnes was fired by the San Diego Padres.