The body of Alesha MacPhail was discovered in woodland on the island in the Firth of Clyde on July 2 last year.
A 16-year-old boy, who cannot be named for legal reasons, denies taking the schoolgirl from her bed, assaulting and murdering her.
He has lodged a special defence of incrimination, stating a named woman committed the crime.
A jury at the High Court in Glasgow heard the child’s naked body was found in the grounds of the former Kyles Hydropathic Hotel at Port Bannatyne.
A post-mortem examination determined the cause of death as “pressure to neck and face”.
Judge Lord Matthews told the panel the case, expected to last up to two weeks, was likely to cause “strong emotions”.
He said: “You have to approach this case with a great deal of professional detachment.”
The teenager, who wore a grey suit in court, denies entering 52 Ardbeg Road with a knife and abducting Alesha.
It is alleged he took her to the site of the former hotel, shook her violently, raped her and inflict injuries “by means to the prosecutor unknown”.
He has pleaded not guilty to a second charge of attempting to defeat the ends of justice by disposing of clothing and a knife on the shore at Rothesay and washing blood off his body.
Agreed statements of fact were read to the jury on Monday before the judge adjourned the case until the following day, when evidence will be heard.