The 69-year-old leader’s announcement came less than three weeks before Turkey holds what is widely viewed as its most important election of the post-Ottoman era.
“Today I will rest at home under the advice of our doctors,” Mr Erdogan said on his official Twitter account.
The President has been campaigning tirelessly to reverse a dip in polls and extend his two-decade election-winning streak.
He is running neck-and-neck with secular opposition leader Kemal Kilicdaroglu and had three campaign appearances planned for Wednesday.
He cut short a live TV interview late on Tuesday after falling ill on air.
Erdogan has been accused of intimidation ahead of Turkish elections amid wave of arrests.
The camera shook and the reporter asking the question stood up from his chair before the broadcast was cut off.
“Oh wow,” an unidentified voice could be heard saying off camera.
Mr Erdogan returned about 15 minutes later to apologise.
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“Yesterday and today were hard work. That’s why I got a stomach flu,” Mr Erdogan said.
“At one point, I wondered if it would be misunderstood if we cancelled the programme. But we promised. I ask for your and our audience’s forgiveness.”
The Turkish leader then took a few more questions before ending the broadcast.