On 13 February 2019, Llorente scored the last goal in a 3–0 Champions League win over Borussia Dortmund, only three minutes after coming off the bench; it was his first career goal in the knockout stages of that competition, and 11th in total. On 17 April, in the same competition, he scored what turned out to be the winning goal in the quarter-final fixture against Manchester City (the tie ended 4–4, Tottenham progressing on the away goals rule). In the second leg of the semi-final away to Ajax, he replaced Victor Wanyama at half time and played a crucial role in helping his team come back from a three-goal aggregate deficit to make it 3–3 and progress again in the same fashion. In the final played in Madrid, he was introduced off the bench with eight minutes remaining and the side already behind, was unable to affect the outcome as Liverpool won 2–0 to take the trophy.