Rapinoe took a knee in 2016 to show solidarity with NFL quarterback Colin Kaepernick, who began kneeling during 'The Star-Spangled Banner' to highlight social inequality and injustice in the USA.
The 33-year-old attacker, who has described herself as "a walking protest", has taken to abstaining from singing during pre-game ceremonies in France.
Trump said in a new interview that it's inappropriate for US Women's Soccer star Megan Rapinoe to protest during the national anthem. He also said the pay gap between the men and women's teams "has to do with the economics." https://t.co/CX0d33hrTH— The Hill (@thehill) June 25, 2019
Asked if he thought USA co-captain Rapinoe's actions were appropriate, Trump told The Hill: "No. I don't think so."
In March, 28 members of the USA women's team filed a gender discrimination lawsuit against US Soccer, citing gaps in pay and resources.
Trump suggested he did not have enough knowledge of the finer details of the issue to take a position.
"I think a lot of it also has to do with the economics," Trump said. "I mean who draws more, where is the money coming in.
"I know that when you have the great stars like [Portugal's Cristiano] Ronaldo and some of these stars … that get paid a lot of money, but they draw hundreds of thousands of people.
"But I haven't taken a position on that at all. I'd have to look at it."
The USA will face hosts France in the quarter-finals of the World Cup after Rapinoe scored two penalties in a 2-1 last-16 win over Spain on Monday.