As Trump consulted national security advisers on whether to reimpose sanctions on Iran and sink the 2015 deal, Macron stressed "the importance of all the signatories to respect it" and called for its "strict application", a statement by the Elysée presidential palace said.
The White House said Trump had "underscored that Iran must stop its destabilising activity in the region", a reference to its influence in Yemen, Syria and Iraq.
Macron said the deal's application should be "accompanied by stronger dialogue with Iran on its ballistic programme and its regional policy, so as to guarantee better security in the Middle East".
Trump is expected to announce on Friday that he believes staying in the deal to be against US interests, as he did last October.
Under the US Iran Nuclear Agreement Act of 2015 he is supposed to inform Congress of his position on the deal every 90 days.
In a joint declaration on Thursday, France, the UK, Germany and the European Union appealed for the agreement to be maintained and said that Tehran has the right to benefit from the lifting of sanctions.
Macron also mentioned North Korea, following his recent visit to China, saying that Pyongyang's resumption of contact with South Korea is "a positive signal", his office said.
The White House statement said that the two leaders "committed to continue to apply pressure on North Korea until it returns to the path of denuclearisation".
It added that Trump and Macron were to meet, schedules permitting, at the World Economic Forum in Davos later this month.