Le Pen declined to answer when asked whether her visit was personal or professional.
Trump team spokesperson Hope Hicks told reporters: "She is not meeting with anyone from our team."
The National Front leader was spotted having coffee at Trump Ice Cream Parlor on the lower-level lobby of Trump Tower with three men including her partner Louis Aliot, the National Front's vice-president.
Also sighted with Le Pen in the Fifth Avenue skyscraper was George "Guido" Lombardi, an Italian businessman who lives in Trump Tower and whom the Politico website described as Trump's "self-professed contact to Europe's far-right parties".
Lombardi said he had introduced Le Pen to entrepreneurs, businessmen, industrialists and diplomats from the United Nations, whom he described as friends and potential donors, in a private gathering at Trump Tower on Wednesday evening.
Russian loan to be repaid
The fourth man was Le Pen's international affairs adviser, Ludovic De Danne.
Le Pen is gearing up to contest the French presidential election with polls predicting that she will qualify for a second-round run-off in May against conservative rival Francois Fillon.
Le Pen has campaigned against immigration, the European Union and globalisation.
Like Trump, she has defended Russian President Vladimir Putin.
Her party has financial worries at the moment since Russia's banking insurance agency has demanded repayment of a nine-million-euro loan made by the First Czech-Russian Bank, which has since collapsed.