Ishaq won his third league and second consecutive title, as they went on to win the 2012–13 Pakistan Premier League, courtesy of Kaleemullah Khan who scored 35 goals in 30 games, most in the history of Pakistan Premier League. Ishaq scored his first league goal of the season on 5 January 2013, after scoring a penalty on 77th minutes against Karachi Port Trust 2–1. Ishaq missed the decisive penalty in a quarter-finals match against National Bank in the 2013 National Football Challenge Cup, causing them to crash out of the tournament.