The White House said Porter denied the allegations and retains the confidence of Trump and his chief of staff John Kelly, but would be leaving his post at an undetermined time.
His resignation comes after reports in the Daily Mail and The Intercept, in which Porter's ex-wives Colbie Holderness and Jennifer Willoughby documented alleged physical and psychological abuse.
A pair of photos showed Holderness with a badly bruised eye, which she claimed was the result of a Porter punch.
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Porter is not well known publicly but is often seen on travels with the president outside Washington and in White House meetings.
In recent weeks he was closely involved in preparations for Trump's address to business leaders in Davos, Switzerland.
The Daily Mail had recently suggested he was in a relationship with Trump's communications advisor Hope Hicks.
"The President and chief of staff have had full confidence and trust in his abilities and his performance," said press secretary Sarah Sanders Wednesday.
She then read a statement from Porter, in which he said "these outrageous allegations are simply false."
"I took the photos given to the media nearly 15 years ago, and the reality behind them is nowhere close to what is being described."
"I've been transparent and truthful about these vile claims, but I will not further engage publicly with a coordinated smear campaign."
