"The Washington Post is far more fiction than fact," Trump tweeted.
The newspaper's story said that Trump has started to bypass Kelly in various ways amid their escalating tension. Kelly reportedly threatened to quit over clashes with the president.
The story about Kelly published on Saturday is based on interviews with over a dozen sources, including administration officials and outside advisers.
"Always quoting sources (not names), many of which don't exist," Trump continued. "Story on John Kelly isn't true, just another hit job!"
Trump often openly attacks media outlets that cover the administration and has called The Post and other news outlets "fake news."
The White House has said that Trump does not plan to participate in this year's White House Correspondents' Dinner. Last year, Trump became the first US president to skip the dinner since 1981.