The defender has signed permanently with Al-Gharafa.
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He leaves the Toffees after 150 appearances and five goals.
Holgate has spent several seasons on loan throughout his Everton career: twice at West Bromwich Albion, including last season, but also with Southampton and Sheffield United.
After playing for the England Under-20 and Under-21 teams, Holgate chose to represent his grandparents' home country, Jamaica, in 2024.
He has made seven appearances for the Reggae Boyz so far.