Thomas Partey has been banned from entering Canada and will miss Ghana’s first World Cup game in Toronto against Panama.
Partey, 32, has pleaded not guilty to seven charges of rape and one count of sexual assault relating to allegations by four different women between 2020 and 2022.
He is due to stand trial next year.
In a statement, FIFA confirmed the former Villarreal midfielder - who played for Arsenal between 2020 and 2025 - will be unable to travel from Ghana's training base in Boston after having his "visa application was refused by the Canadian government".
World football's governing body, added: "FIFA is not involved in the immigration processes of host countries, including the adjudication of visas.
"The host government ultimately determines who receives a visa and is admitted into the country."