In his second season at Manchester United, Romero continued to be the first choice goalkeeper in cup competitions, including the club's Europa League campaign, which new manager José Mourinho explained that he deserved to play in. Romero kept his first clean sheet of the season on 29 September 2016, in a 1–0 win over Zorya Luhansk. Romero's performance in a 4–0 win over Feyenoord was praised by pundits. Following this, Romero kept three more clean sheets in the UEFA Europa League matches, in which he kept two in both legs against Saint-Étienne. In the second leg of a match against Rostov, Romero made a crucial save from Christian Noboa’s free-kick, which helped Manchester United progress to the next round. Romero rejected a move back to his homeland with Boca Juniors in the January transfer window. Romero played in the 2017 Europa League final in which he kept a clean sheet in a 2–0 victory over Ajax.