A drop in income after sponsors - and huge legal bills after the corruption scandal - has seen the world governing body hit hard in the pocket. FIFA's executive committee members were told the losses for the year totalled 103 million Swiss francs, according to insiders.
FIFA have so far been unable to replace top tier partners Emirates and Sony - plus second tier sponsors Castrol, Continental, Johnson & Johnson - due to the toxic brand.
The revelation of the deficit will put pressure on FIFA's ExCo members to vote for proposed reforms at a meeting in order to attract new sponsors. The organisation has already made significant savings to reduce the level of the deficit.
FIFA's income always drops in the year after World Cups but it has always previously managed to make a surplus - in 2011 it made a $49.2 million profit, which was added to their reserves currently totalling some $2.05 billion.
The legal bills are also significant - suspended president Sepp Blatter brought in a team of American lawyers after the US justice department announced their indictments of 18 officials on football-related corruption charges in May. Blatter and other senior FIFA executives are also believed to be under investigation by the FBI.
FIFA's last annual deficit came in 2001 when the bankruptcy of its marketing partner ISL saw the world governing body end the year in the red and forced to take out a $241 million bridging loan.
The proposed reforms to be voted on at FIFA's ExCo meeting include 12-year term limits for the president and ExCo members, financial transparency including the salary paid to the president and senior officials, plus some independent members sitting on the ruling committee.
Michel D'Hooghe, the Belgian who is the FIFA ExCo's longest-serving member, said that the future of the organisation depended on the reforms being passed.
D'Hooghe said: "Don't think that FIFA is dead. I have the assurance that if FIFA and the Congress can accept the reforms then FIFA has a good future. But we must know that this is a deep crisis, we must accept that and approach that with great humility.
"This is a difficult moment financially but the expectations are good I'm sure in the longer term FIFA will overcome that."