Brannigan arrived at Villa from Linfield in the summer of 2023, penning his first professional contract a year later.
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Villa academy chief Mark Harrison said: “We are delighted to see Cole sign an extension to his contract.
“He was a key performer in the Under-18s last season, and played a significant part in their success with his goals and assists.
“He is a technically efficient, creative player who links and combines the game well.
“We look forward to seeing how he develops over the coming seasons.”