Shane Hughes, 31, allegedly abused the girl 15 times over four months in a physiotherapy room, where she was supposed to be getting treatment for a knee injury.
Prosecutor John Livingstone told the court that the first attack happened after he told her to take her clothes off and get on the massage table.
Mr Livingstone added: 'She said "No, what is happening?" He then pushed her back on the massage table and told her not to scream and, though she did, he put his hands over her mouth and forced her clothes off.'
It alleged that he raped the girl and forced her to perform a sex act, Kingston Crown Court heard.
Hughes, who is the Premier League club's children's coach, is said to have carried out the offence in 2011 at their training headquarters in Cobham, Surrey.
The girl is now 16 years old, and Hughes is facing 14 counts of rape in relation to a child under the age of 13. He however denied raping her while the case was adjourned for continuation.