The 68-year-old had said he would stand for a further year but said on Thursday that opposition to proposed governance reform to the FA council had caused him to reconsider.
"What I now see is that even if we get the reform through (which will be a difficult and divisive process although essential), I am probably not the best person to pick up the pieces following the inevitable discord," he said in a statement.
Dyke, a prominent opponent of FIFA president Sepp Blatter during the recent corruption scandal within world football's governing body, took over from David Bernstein in 2013.
(Reporting by Toby Davis; editing by Dominic Evans)
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