Dr Stephen Hamilton, 45, from Altrincham, Greater Manchester, is alleged to have given the girl the anti-depressant citalopram before abusing her.
Manchester Crown Court heard how he would put his hands around the girl's neck as he attacked her and told her 'you deserve to die'.
The historic offences are alleged to have occurred over two-and-a-half years between 2006 and 2009.
Dr Hamilton, who is a GP and partner at Bolton's Heaton Medical Centre, was arrested after the girl, who cannot be identified for legal reasons, complained to a teacher in November 2011.
She went on to describe the alleged abuse in graphic terms to police, claiming that the GP would 'restrict her breathing' and 'taunted her' as he raped her.
The victim alleges that she suffered 'nightmares' about Dr Hamilton as a result of the alleged abuse.
Opening the case, prosecutor Louise Blackwell QC told the jury: "In essence, what she described is that he controlled her in every way possible - including secretly medicating her."
The court heard that a colleague at Dr Hamilton's practice reported him to the General Medical Council when he learnt that he had prescribed the girl citalopram, an anti-depressant not licensed for children.
Dr Hamilton denies six charges of rape, three charges of sexual assault, four charges of child cruelty and a charge of administering a noxious substance.
Miss Blackwell added: "He threatened (the girl) that if she ever told anyone about anything of the sexual abuse that was taking place, that he would prove that she was making it up."
Judge Richard Mansell QC warned the jury to 'adopt a calm, dispassionate attitude' to the evidence during the trial, which is expected to last up to four weeks.
He said: "Allegations of sexual offending, especially rape, can cause people to experience a range of emotions.
"It can engender feeling of sympathy or pity, outrage and disgust. Bear in mind these remain allegations unless and until you as a jury of 12 decide so that you are sure that the defendant is guilty of one or more of the allegations.
"Do not allow such feelings, if you have them, to affect your judgement in this case."
The trial continues.