At the start of the 2012–13 season, Haroun made three league starts before being fringe from the first team for a month. He then started six league matches between 6 October 2012 and 6 November 2012. Haroun scored his first goal for Middlesbrough in the 2012–13 season against Hull City, in which he dribbled around the keeper in a 2–0 victory. However during a 1–0 loss against Cardiff City on 17 November 2012, Haroun suffered a calf injury and was substituted in the 30th minutes. After the match, it was announced that he was sidelined for two weeks. It wasn't until on 8 December 2012 when Haroun returned to the starting line–up against Peterborough United and scored his second and third goals of the season in a 3–2 win. However, during the match, he suffered a hamstring injury and was substituted as a result; which saw him sidelined for a month. It wasn't until on 12 January 2013 when Haroun returned to the starting line–up, in a 2–1 loss against Watford. A month later on 16 February 2013, he scored his fourth goal of the season, in a 4–1 loss against Crystal Palace. Later in the 2012–13 season, Haroun later found himself in and out of the starting line–up, which saw him placed on the substitute bench. He finished the season, making twenty–nine appearances and scoring four times in all competitions.