
The decision has come by mutual consent, with the Welshman set to bring the curtain down on his second spell with the Swans.
Margetson first joined in 2019, and was part of Steve Cooper's staff before leaving in 2021.
During that stint he was also part of Gareth Southgate's England set-up, after stepping down from his role with Wales in 2016.
He re-joined the Swans in 2023, and returned to the Wales national team a year later to work under under Craig Bellamy.
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During his five seasons with the club, he has been credited as key figure in the development of keepers like Freddie Woodman, Carl Rushworth and Lawrence Vigouroux.
“For me Marge (head of goalkeeping Martyn Margetson) has been so instrumental with everything that we do day to day," Vigouroux said about Margetson earlier this season.
“So I feel very lucky and I feel blessed to have those people around me, and then being part of such a great dressing room.
"Long may that continue."
His exit means Swansea will now need to appoint a successor before the 2026-27 season.
In a statement, the club said: "Swansea City thanks Martyn for his services to the club across his two spells.
"We wish him well for the future and he will always receive a warm welcome at the Swansea.com Stadium."