"Congratulations to the U.S. Women's Soccer Team on winning the World Cup! Great and exciting play," Trump tweeted.
The US defeated the Netherlands 2-0 on a penalty by Megan Rapinoe and a strike by Rose Lavelle in the final in Lyon.
Rapinoe had earlier vowed to stay home if Trump invites the team to Washington, and she urged her team-mates to join her in protesting the president's policies and character.
Trump responded on Twitter that "Megan should never disrespect our Country, the White House, or our Flag, especially since so much has been done for her & the team."
Championship US sports teams are traditionally honoured with an invitation to the White House, though Trump has at times revoked invitations after team members criticised him.
Among the teams that have declined the offer have been pro basketball's Golden State Warriors and last year's Super Bowl winners, the Philadelphia Eagles of the National Football League (NFL).