Boyd started in Burnley's first game back in the top flight to open the 2016–17 season, playing the whole match in a 1–0 home defeat to Swansea City. His running statistics were once again highlighted during the season when he had run 58.3 miles in Burnley's opening seven fixtures, five percent more than Jordan Henderson in second place. He scored his first goal of the season in a 3–2 home win over Bournemouth on 10 December 2016, latching onto Andre Gray's backheel before finishing low into the corner of the goal. Boyd scored in Burnley's crucial 1–0 victory against Stoke City on 4 April 2017, ending a run of seven games without a win when he swept home Jeff Hendrick's cross to score the only goal of the game. He played in 36 of Burnley's 38 Premier League fixtures that season as they secured safety after finishing in 16th position, scoring twice. In April 2017 he was in contract talks with Burnley with his contract running out in the summer. Further talks took place in May, although ultimately no contract extension was agreed. He made 123 appearances during his three-year tenure at the club, scoring 12 goals.