The nominees for FIFA's 'The Best' Women's Player of 2017 were Carli Lloyd, Lieke Martens (winner) and Venezuelan Deyna Castellanos, 18, who does not play in a professional league.
USA's Rapinoe, who won the World Cup in 2015, told the 'BBC': "The award just doesn't hold a lot of weight when you've got someone on the list I've never heard of."
"It signals to us and it signals to the rest of the world that Fifa doesn't really care," she said.
FIFA turned to their selection process to defend themselves. A statement read:
"The process is clear and transparent and we are not involved in the final selection of nominees.
"However, we have taken note of the concerns raised by the football community and our fans and will take this feedback on board in future editions of The Best Awards."
But Rapinoe hit back by saying: "If some random male player, who was not even a full professional, was nominated, I'm sure they would step in for that, so it's disappointing that the same hasn't been done for us."