Mr Hannity had tweeted Monday morning that he was not going to speak at the final Trump rally before the election.
He wrote: “In spite of reports, I will be doing a live show from Cape Girardeau and interviewing President Trump before the rally.
“To be clear, I will not be on stage campaigning with the President.
“I am covering the final rally for my show. Something I have done in every election in the past.”
Mr Hannity’s colleague Jeanine Pirro also spoke at the rally.
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Upon taking the stage, Mr Hannity pointed at all of the media and said: “By the way, all of those people in the back are fake news.”
This was greeted by cheers from the crowd as Trump smiled.
Trump responded: “I don’t want to insult.”
He added that some of the media in the back were “fine”.
Later, Trump introduced Ms Pirro as she took the stage.
He said: “There’s a woman on Saturday night that treats us very, very well.
“And she does it with love and with passion for the country. No for me, it’s not passion for me, it’s a passion for the country.”
Mr Hannity interviewed Trump following the rally.
A Fox spokesperson denied giving Mr Hannity approval to speak at the rally.
Fox did not broadcast Mr Hannity’s rally appearance despite promising to cover the entire event.
On Twitter, users have had mixed reactions to Mr Hannity’s appearance.
One user spoke highly of the anchor, calling him an “American Hero”.
While another commented: “Oh It’s like a contest.
“Who can lie more often: Donald Trump or his side-kick Sean Hannity.”
Annoyed at the apparent backtrack from his Twitter statement, a third said: “OMG. The constant lying is exhausting.”
Demanding an explanation, someone else asked: “Hey Lying Sean Hannity…Care to explain?”