The prestigious magazine offered no details on the allegations against Lizza, 43, the latest media figure to face consequences amid a wave of harassment allegations surfacing in recent weeks.
"The New Yorker recently learned that Ryan Lizza engaged in what we believe was improper sexual conduct," the magazine said in a statement.
"We have reviewed the matter and, as a result, have severed ties with Lizza. Due to a request for privacy, we are not commenting further."
"I am dismayed that The New Yorker has decided to characterise a respectful relationship with a woman I dated as somehow inappropriate," Lizza was quoted as saying.
More From This Section
"The New Yorker was unable to cite any company policy that was violated."
The law firm representing Lizza's accuser -- who wishes to remain anonymous -- issued a statement of its own, pushing back at his version of events and saying that "in no way did Mr Lizza's misconduct constitute a 'respectful relationship' as he has now tried to characterise it."
CNN, where Lizza has been a contributor, said the writer would not appear on the news channel "while we look into this matter."
Earlier this year, Lizza's report from an interview with Scaramucci ended the brief White House career of the longtime Wall Street banker.
The article stemmed from an expletive-laden interview with the former hedge fund manager who lasted just 10 days in the White House.