While the terms of the deal remain confidential, the club has secured a substantial fee with potential for significant future add-ons and a sizeable sell-on clause.
A St Mirren Youth Academy graduate, Mooney made 23 appearances for the Buddies since making his first-team debut in October 2024, scoring one goal in a 3-2 win over St Johnstone in the William Hill Premiership.
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Saints boss Stephen Robinson told the official club website : "It's a fantastic opportunity for Evan at a club the size of Arsenal.
"It was a terrific deal for the club as well and we're very well protected in terms of adds on and sell on should Evan go on to fulfil the potential that we believe that he has.
"Evan, his family and advisers were very keen to go to Arsenal and we wish him nothing but good luck