The 2012–13 1. FC Köln season is the 64th season in club history. In 2012–13 season, the club plays in the 2. Bundesliga; the second tier of German football. It is the clubs first season back in this league, after it was relegated from the Bundesliga in 2012. The season started on 5 August 2012 and is scheduled to end on 19 May 2013.

The club is taking part of the 2012–13 edition of the 2. Bundesliga and the 2012–13 edition of the DFB-Pokal. The season started on 5 August 2012 with a loss against Eintracht Braunschweig and ended on 19 May 2013 against Ingolstadt 04.

The club started their league season with a six-match winless streak. Their first league win came against FSV Frankfurt on matchday seven. Overall, The first victory came against SpVgg Unterhaching in the opening round of the cup.

Holger Stanislawski was hired as the new head coach on 14 May 2012.

1. FC Köln was hit with a €50.000 fine. The club was only allowed to sell 15.000 tickets to its own supporters and a maximum of 5.000 tickets to supporters of SV Sandhausen. The club stated that this is an economic loss of approximately €500.000. The club appealed the decision and will only pay €40.000 fine and the maximum number of tickets that can be sold to its own supporters was increased to 22.500.

There have been repeated rumours about the club being in a grave financial situation. In a letter to club supporters, the club stated "The current financial position of the 1st FC Köln is serious. However, we also want to use this letter to continually eliminate repeated rumors that are without substance. An over-dramatizing the situation is just as damaging as to trivialize it." The club stated that they'll be using revenue bonds for debt restructuring.

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