Eight posters featuring Rapinoe in his US National Women's Team jersey included homophobic and defamatory insults, as well as the phrase "screw it on," the NYPD told CNN.
The incident was reported Monday morning around 7:15 am at West 42nd Street subway station.
"Hatred has no place in the transit system and we are working hard to make the subway a welcoming and safe environment for all," said the deputy director of communications. MTA, Shams Tarek, in a statement.
The posters have been cleaned "and we will have them replaced with new ones if necessary," added Tarek.
At the rally after the parade, Rapinoe, who won the Golden Boot and Golden Ball tournament, was awarded to the top scorer and the most valuable player in the contest.