The election for the President of FIFA was held at the congress, with the incumbent, Joseph "Sepp" Blatter facing a challenge from the Cameroonian football executive and president of the Confederation of African Football, Issa Hayatou. Blatter won with 139 of the 195 votes cast. Like the previous presidential election at the 51st FIFA Congress, this congress was overshadowed by accusations of fraud and corruption after 11 members of FIFA's Executive Committee had filed a criminal complaint against Blatter with courts in Zurich.
A question and answer session was held at the congress the day before the election in which Blatter refused to allow Hayatou and the FIFA Vice-President David Will to take part. Delegates booed Blatter afterwards and Blatter and Hayatou were involved in a verbal confrontation. Will was described as "shaking with rage" by reporters.