Joe, who died in April aged 36 after a third cancer fight, will be remembered at Old Trafford with an annual award in their academy.
The Joe Thompson Award, Man Utd announced, will be presented to a player or staff member from their under-18 or under-21 sides.
"It will be given to somebody who represents the values of a Manchester United person, like Joe did, displaying characteristics like resilience, honesty, integrity, humility, innovation and a relentless work ethic, with a focus on the community," Man Utd said in a statement.
"This new award will act as a lasting tribute to Joe, whose story of courage, perseverance and positivity touched the hearts of fans all around the world."
Joe came through Man Utd's academy before going on to play for clubs including Rochdale, Bury, Tranmere Rovers and, in 2015/16, Carlisle.
Joe Thompson played for Carlisle in the 2015/16 seasonJoe Thompson played for Carlisle in the 2015/16 season (Image: Barbara Abbott)
During his career he faced two battles with Hodgkin Lymphoma, with the disease returning for a third time in retirement.
The courage and character he showed throughout his life proved hugely inspirational.
Man Utd added: "Joe’s passing was announced on 18 April and his loss has been sorely felt across the club, and indeed the wider football community.
"With the Joe Thompson Award, we intend to keep his legacy alive."
The first winner is set to be announced next week.
Joe made 17 appearances for Carlisle after joining United under Keith Curle in the summer of 2015.
He remained close to many of his Blues team-mates in subsequent years and always spoke fondly of his time in Cumbria.
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