General manager Chuck Fletcher will add president of hockey operations to his title and report directly to chairman and CEO Dave Scott.
Holmgren just completed his 40th year with the organization. He played for the Flyers from 1975-84, was an assistant coach from 1985-88, head coach from 1988-92, general manager from 2006-14, and president from 2014-19.
"It's been an honor to serve this franchise in many different roles throughout my life and I look forward to this next chapter," said Holmgren. "I approached Dave about my idea to step aside to spend more time with my family. I have complete confidence in Chuck in his new role, leading the Flyers to great things."
The Flyers missed the playoffs just twice under Holmgren's reign as general manager, reaching the Stanley Cup Final in 2010.
Holmgren was unafraid of big moves - for better or worse. In 2009, he signed Chris Pronger to a massive seven-year extension. On June 23, 2011, he shook the hockey world by trading away core pieces Mike Richards and Jeff Carter and signed Ilya Bryzgalov to a nine-year contract. He also inked Shea Weber to a 14-year, $110-million offer sheet in 2012, which the Nashville Predators matched.