The 25-year-old joined Boro from Plymouth Argyle for £5m in January 2025 and scored 14 goals in 66 appearances.
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Whittaker finished last season as Middlesbrough’s leading scorer after a remarkable turnaround, ending a 25-game goal drought before scoring eight times in 12 matches, including goals in six consecutive games.
He had made five appearances this season, starting all three Championship games before the victory over West Bromwich Albion.
Middlesbrough have signed 12 players this summer, including Brighton loanee Amario Cozier-Duberry, as they continue reshaping their squad following last season’s failure to reach the Premier League.