Hinch, a former manager of the Arizona Diamondbacks, is departing to pursue other opportunities in baseball, effective immediately.
"I want to thank A.J. for his hard work and commitment to the Padres over the past four years," said Padres executive chairman Ron Fowler in a statement Tuesday. "He has represented the organization well, and we wish him nothing but the best in his future endeavors."
Hinch was working with assistant GM Fred Uhlman Jr. and senior vice president of baseball operations Omar Minaya to direct the club's baseball operations in the wake of the June firing of general manager Josh Byrnes.
"During my time in San Diego, I dedicated myself to do everything I could to help this team win, in the short-term and for the long-term," said Hinch. "These last several weeks were no exception. I think the organization is ready for a transition and I've made a decision and told Ron Fowler and (team president) Mike Dee that now is the right time for me to move on. I'm proud to have always operated in the best interest of the organization and to have established long lasting relationships with people who work on and off the field in San Diego. I wish the Padres and the new GM well in the future and look forward to the next chapter of my baseball career."
Hinch joined the Padres in September 2010 as vice president of pro scouting and moved into his role as assistant GM a year later. He was the manager of the Diamondbacks from May 8, 2009 through July 1, 2010 when Byrnes was Arizona's GM. He and Byrnes were fired in Arizona on the same day.