Rapinoe, 30, starred during the Americans' run to the Women's World Cup this past summer and is among the finalists for the FIFA World Player of the Year award.
U.S. Soccer said Rapinoe's injury was confirmed by an MRI scan after she was hurt in Honolulu, but no time frame was given for her recovery.
"I want to thank my teammates and the staff for the amazing support I've received so far," Rapinoe said in a statement. "I know I'll be in the best of hands moving forward and I'll be doing everything I can to get healthy as soon as possible.
"This is obviously a very difficult time, but I do feel super confident in my recovery as I've gone through this before and I know what the process will be like. I want everyone to know that I'll be fine, and that I'm currently accepting any recommendations for TV shows to binge watch and great restaurants that deliver in Seattle. I'm also going to get really good at FIFA 16."
The serious injury could potentially rule out Rapinoe for next summer's Olympics in Rio de Janeiro.
"All of our hearts feel for Megan and she's certainly a major part of this team, both on and off the field, so to see her go down is tough," U.S. coach Jill Ellis said. "Players getting injured is always hard, but all of her teammates know that one of the strengths of this team is depth and everyone in the player pool is prepared to step up as we continue to prepare for Olympic qualifying.
"Megan has a great support system and she's very resilient, so we know she will be back as soon as possible."
Rapinoe tears ACL
United States soccer midfielder Megan Rapinoe tore her ACL during training. Julie Foudy of espnW gives the inside scoop on if she will be able to play in the Rio 2016 Olympics.