Aldo Rebelo said he would make way for someone new after delivering the 12 stadiums to be used in the tournament, all of which are due to be ready by December.
A federal congressman with the Communist Party, Rebelo took over in 2011 after his party colleague was forced to resign due to allegations of corruption.
Rebelo was at the centre of a diplomatic incident last year when he refused to meet with FIFA secretary general Jerome Valcke, who said Brazil's preparations were too slow and needed a "kick up the backside."
Rebelo said he was resigning to run for office in next October's elections.
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- Aldo Rebelo