There are several clubs playing in Linköping but there is one big rivalry to FC Linköping City and that is the games against AFK Linköping, a club that was also founded in the winter between the 2012 and 2013 season. The difference is that FC Linköping City built their team with players from higher leagues and AFK Linköping used more local talents. The first game played between these rivals were played away June 19, 2013; a game where FC Linköping City won 2–0. The return game in the league was played at home on August 4, 2013 in the new arena Linköping Arena and FC Linköping City won with the same 2–0 score as the first meeting.
In 2013 FC Linköping City immediately put up the goal to win Division 3 and get promoted to Division 2. The start of the season started promising and the club had seven consecutive wins before drawing 3–3 away against Linghems SK. This seven game winning streak is even more remarkable due to the fact that only two out of seven games were at home. When Division 3 reached its summer break the club had a five point lead with a 9–1–1 record (9 wins, 1 draw, 1 loss) and nine games left at home and only two games left away. The second part of the season was even more impressing when they won all remaining eleven matches and saw the lead grow to the final 22 points ahead of second placed team IF Haga. This meant promotion to Division 2 (tier 4 of Swedish football) and a good start for the newly built club aiming for the top Swedish football.
Before the season started FC Linköping City announced a change of head coach in the continued goal of advancing in the league system. The new coach Andreas Thomsson comes from Öster IF in Allsvenskan (tier 1 in Swedish football) and has merits from football on the highest level in Sweden.