The former England captain has returned to cricket during the past year after a horrific car crash while he filmed for the BBC's Top Gear television programme at the end of 2022.
He served as an England assistant coach during this year's T20 World Cup and oversaw the Northern Superchargers in the most recent edition of English domestic cricket's Hundred competition.
The 46-year-old former all-rounder is currently with the Test side at the Oval for this week's series finale against Sri Lanka, standing in for batting coach Marcus Trescothick, and he has now agreed to take over the second-string Lions for the next four series.
The aim of the Lions is to develop emerging talent for the senior squad, with Flintoff signing up for tours of South Africa and Australia as well as home fixtures against India A and Zimbabwe.
"I'm incredibly excited to take on this role with the England Lions," said Flintoff. "It's a fantastic opportunity to work with some of the best up-and-coming talent in the country and to help shape the future of the men's game.
"The Lions programme has always been a vital stepping stone for players pushing for international success, and I'm honoured to be part of that journey."
Flintoff, who recently presented a well-received second series of Field of Dreams on BBC television, where cricket is used to help disadvantaged youngsters, added: "The future of the game in England is in excellent health. There is a wealth of talent emerging, and I'm looking forward to helping these players reach their full potential.
"It's an exciting time for English cricket, and I'm passionate about inspiring the next generation to take the sport forward. We've got a strong foundation, and I believe we can create something truly special."
Flintoff has been tipped as a future England head coach by director of cricket Rob Key, a former international team-mate.
Ed Barney, men's performance director at the England and Wales Cricket Board, said: "We are thrilled to welcome Andrew Flintoff into this key role. Andrew stood out thanks to his inspirational leadership, coaching expertise, and deep understanding of the game."
