The duo, who have not been named but are both understood to be 20 years old, are due to appear in court on the Balearic holiday island.
It is alleged the rape was carried out by one of the players while the other filmed it on a mobile phone.
The British teenager was allegedly attacked in the early hours of Tuesday, reported the local paper Periodico de Ibiza.
Spanish police are hunting for a third player and teammate accused of abducting the British woman before she was raped in Cala de Bou hotel.
Local reporter Paco Perez said Spanish criminal forensic investigations had confirmed she had been sexually attacked and that she was known to her attackers.
The two footballers were held in custody at a local police station ahead of an expected closed court hearing in front of an investigating magistrate tomorrow.
Mr Perez said the duo play for Charlton, and added: “One has been charged with rape and the other with filming the attack on a mobile phone.”
He said a judge has requested the arrest of the players by the Family and Women Unit of the National Police of Ibiza.
A Spanish National Police spokesman confirmed two British 20-year-olds had been arrested on suspicion of sexually assaulting a 19-year-old Brit.
The spokeswoman said they were currently at a police station in Ibiza and would appear in court this afternoon or tomorrow morning.
She said: “I can confirm two British men aged 20 have been arrested on suspicion of the sexual assault of a 19-year-old British woman. They are still in police custody.”
The spokeswoman would not say if they were footballers, adding: “It is not something that we would confirm.”
Cala de Bou is a popular location for tourists near party town San Antonio just seven miles from the airport.
Periodico de Ibiza reported a group of players had invited the alleged victim and a girlfriend back to their hotel after meeting them during a night out in San Antonio.
Reporting from SWNS by Berny Torre and Paco S Pérez