Messi was named the Best Men’s Player for a record sixth time, while Rapinoe won the Best Women’s Player after inspiring USA to World Cup glory.
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Virgil van Dijk had been favourite for the men's prize heading to the ceremony in Milan after guiding Liverpool to Champions League glory in June.
However, it was Messi – who won La Liga with Barcelona but lost to Liverpool in the Champions League semi-finals – that took home the prize ahead of Van Dijk and Cristiano Ronaldo.
Messi scored 36 goals in 34 league games last season, making him Europe's top domestic goalscorer for the third straight season.
He was also the top scorer in the Champions League with 12 goals in 10 games.
Ronaldo won Serie A with Juventus and the Nations League with Portugal, but falls one behind Messi in terms of FIFA awards, having last won in 2017.
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Rapinoe was the USA’s standout player at the World Cup in France, claiming the Golden Boot and Golden Ball after scoring six goals.
The 34-year-old also made headlines when stating she was “not going to the f***ing White House” to meet President Donald Trump should they win the trophy.
Trump went on to invite the team “win or lose”, although Rapinoe reiterated her stance after the victorious squad touched back down in the US.
Rapinoe has described Trump as “sexist” and “misogynistic” in the past, and went to claim the US President’s style was excluding marginalised Americans.
The Best FIFA Men’s Goalkeeper award went to Liverpool’s Alisson Becker, with the Brazilian beating Manchester City’s Ederson and Marc-Andre ter Stegen to the award.
Sari van Veenendaal (Netherlands/Arsenal/Atletico Madrid) won the Best FIFA Women’s Goalkeeper ahead of Christiane Endler (Chile/Paris Saint-Germain) and Hedvig Lindahl (Sweden/Chelsea/VfL Wolfsburg).
FIFPro World XIs
Men’s World XI: Alisson Becker (GK), Matthijs de Ligt (DEF), Sergio Ramos (DEF), Virgil van Dijk (DEF), Marcelo (DEF), Luka Modric (MID), Frenkie de Jong (MID), Eden Hazard (MID), Cristiano Ronaldo (FW), Kylian Mbappe (FW), Lionel Messi (FW)
Women’s World XI: Sari van Veenendaal (GK), Lucy Bronze (DEF), Nilla Fischer (DEF), Kelley O’Hara (DEF), Wendie Renard (DEF), Julie Ertz (MF), Amandine Henry (MF), Rose Lavelle (MF), Marta (FW), Alex Morgan (FW), Megan Rapinoe (FW)
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