He was struck on the face by a coin thrown by a West Brom supporter on 20 February 2016 in an FA Cup Fifth Round tie at Championship side Reading. Brunt was appalled by the incident, stating: "If people come to football matches and think it is acceptable to throw coins at footballers or anyone else, it is disgusting."
Brunt returned to first-team action after eight months out with an anterior cruciate knee injury in the 1–1 draw against Tottenham Hotspur at The Hawthorns on 15 October 2016. He scored his first goal of the 2016–17 season on 3 December in a 3–1 home win over Watford, ending a run of 29 Premier League appearances without a goal. His second goal of the season came on 2 January 2017 in a 3–1 home victory against Hull City, when he headed in from a Matt Phillips corner kick. 12 days later, he made his 300th league appearance and 200th Premier League start for West Brom in the next fixture against Tottenham Hotspur at White Hart Lane which ended in a 4–0 defeat for the West Midlands club. On 9 February 2017, Brunt signed a contract extension which would keep him at the club until the summer of 2018 with an option for another year should he trigger a clause relating to appearances. He made his 500th career appearance in club football against Burnley in August 2017 and the following month made his 350th appearance for Albion, against Watford.
He missed out on the chance to appear at Euro 2016 after damaging his anterior cruciate ligament which required surgery. On 11 November 2016, Brunt returned to the international scene for Northern Ireland's 2018 World Cup qualification match against Azerbaijan. After sustaining a head injury early on, he recovered to set up a goal for club teammate Gareth McAuley and scored the final goal of a 4–0 win.