The Journal reported the letter was one of several included in a leather-bound album meant to celebrate Epstein's 50th birthday, about three years before sex-abuse allegations emerged against the financier.
Reuters could not immediately confirm the authenticity of the letter.
Trump quickly responded to the story on his Truth Social platform, saying he would sue the newspaper and Rupert Murdoch, who controls its publisher, News Corp.
"The Wall Street Journal, and Rupert Murdoch, personally, were warned directly by President Donald J. Trump that the supposed letter they printed by President Trump to Epstein was a FAKE and, if they print it, they will be sued," Trump wrote. "President Trump will be suing The Wall Street Journal, NewsCorp, and Mr. Murdoch, shortly."
A spokesperson for the Wall Street Journal and its parent company, Dow Jones & Co, declined to comment on its story or Trump's threat to sue. Representatives for News Corp and Murdoch could not immediately be reached for comment.
The White House did not immediately respond to a request for comment from Reuters.
The Journal said the letter, bearing Trump's name, contains several lines of typewritten text framed by the outline of a naked woman, which appeared to be hand-drawn with a heavy marker.
The newspaper said the letter concludes "Happy Birthday - and may every day be another wonderful secret", and featured the signature "Donald".
Vice President JD Vance responded to the story on social media platform X, saying, "Forgive my language but this story is complete and utter bullshit. The WSJ should be ashamed for publishing it."
The White House has been roiled by questions about disgraced financier and convicted sex offender Epstein, after the Justice Department concluded there was no evidence to support a number of long-held conspiracy theories about his clients and 2019 death in prison.
Attorney General Pam Bondi had pledged months earlier to reveal major revelations about Epstein, including "a lot of names" and "a lot of flight logs".
Some Trump supporters have demanded the release of more information on Epstein, causing a rare fracture within his base of support.
Trump posted shortly after foreshadowing legal action that he had asked Attorney General Pam Bondi to produce all pertinent grand jury testimony in the Epstein case, subject to court approval.
"Based on the ridiculous amount of publicity given to Jeffrey Epstein, I have asked Attorney General Pam Bondi to produce any and all pertinent Grand Jury testimony, subject to Court approval. This SCAM, perpetuated by the Democrats, should end, right now!" Trump wrote on Truth Social.
Soon after, Bondi said on X that the Justice Department was ready to move the court on Friday, US time, to unseal the grand jury transcripts.
"President Trump - we are ready to move the court tomorrow to unseal the grand jury transcripts," Bondi wrote.
Allegations that Epstein had been sexually abusing girls became public in 2006 - after the birthday book was compiled - and he was arrested that year before accepting a plea deal.
Epstein died in 2019 in jail after he was arrested a second time and charged with sex-trafficking conspiracy.
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