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Houghton, 27, has played a pivotal role in Hull's success in 2016 as Lee Radford's side chase a domestic treble.
He has made 1,130 tackles in 2016, more than any other player in Super League.
"I've tasted success winning the Challenge Cup and I want to do that over and over again," Houghton told the club website.
Hull FC hooker and vice-captain Danny Houghton has signed a new deal with the Challenge Cup winners and will stay with the club until 2020.