The call was scheduled to congratulate Peggy Whitson on breaking the record for longest time spent in space by an American astronaut.
Whitson had specified that a bill signed by Trump in March authorizing $19.5 billion in funding for NASA directed the agency to send astronauts to the planet during the 2030s.
She called the space station "a key bridge" between living on Earth and travelling into deep space, and she singled out the station's recycling system which transforms astronauts' urine into drinking water. Whitson mentioned the recycled urine process during a live interview with the President, but she's also spent more than 53 hours of time doing spacewalks and extra-vehicular activity.
"I'm glad to hear that", Trump responded. "On behalf of our nation and, frankly, on behalf of the world, I'd like to congratulate you".
The world record - 879 days - is held by Russian astronaut Gennady Padalka.
"Well it's actually a huge honor to break a record like this, but it's an honor for me basically to be representing all the folks at NASA who make this spaceflight possible and who make me setting this record feasible", Whitson told the President.
Whitson, who has been on board the ISS since November 2016, is also commanding the space station for the second time.
A banner flying behind her read: "Congrats Peggy!"
President Trump, astronaut Kate Rubins (L) and daughter Ivanka (R) during a video conference with NASA astronauts aboard the International Space Station.
"What are we learning from having you spending your time up there, I know so much research is done - I'm getting a glimpse of it right here in the Oval Office - what are we learning by being in space?"
When Whitson was little, she had no female astronauts to look up to. The date will depend on whether astronauts are on board for the test flight, which could hoist the new Orion capsule to the vicinity of the moon.
He asked the two astronauts whether they were ready to go to Mars.