The appointment of José Mourinho as manager led to Young's game time being limited in the first half of the season. His first appearance was on 15 September 2016 in the Europa League against Feyenoord, coming on as a 63rd-minute substitute for Juan Mata in a 1–0 loss. His first start was against Northampton Town in the EFL Cup on 21 September, with Young playing on the wing in a 3–1 victory. Young featured in the next two games as a substitute, against Leicester City in a 4–1 league victory on 24 September and on 29 September against Zorya Luhansk in a 1–0 win in the Europa League. From October to January, Young managed to only make four appearances – all of which came as starts at wing back or at full back. Despite being limited for chances, one of these came against rivals Liverpool on 17 October, in a 0–0 draw at Anfield. His next start came against Blackburn Rovers in the FA Cup on 19 February 2017, playing the full 90 minutes in the 2–1 away win. After this game Young started to play far more regularly, featuring heavily in March and April. He was an unused substitute for the 2017 EFL Cup Final against Southampton on 26 February, which United won 3–2. Young made his first assist of the season on 19 March against Middlesbrough, crossing the ball to Marouane Fellaini, who headed in the opening goal of a 3–1 victory. On 16 April, Young captained Manchester United for the first time in a 2–0 win against Chelsea. His season ended after suffering an injury against Celta Vigo in the Europa League semi-final first leg on 4 May, after coming on for Henrikh Mkhitaryan in the 78th minute.