The boy – who cannot be named for legal reason – is said to have pounced on the girl just 300 yards from her home.
Her mum texted her “where are you” when she was late coming home from school.
Minutes later there was a knock on the door from a passerby who had found the girl lying in the stream, the court heard.
She was barely conscious, with her underwear pulled down, and was wet and muddy from the attack.
The accused has pleaded guilty to choking and sexually assaulting the girl, but denies rape and attempted murder.
“He’s a 16 year-old who was in mainstream education but, as you’ll hear, was diagnosed as autistic”
Richard Smith QC
Bristol Crown Court also heard the boy denies he wanted to choke the girl unconscious so he could rape her.
Jurors were told the boy left school on his bike and then pounced on the girl on his way home in Exmouth, Devon.
The jury was shown a police interview with the victim in which she described pretending to be dead during the assault.
She was attacked after the boy dragged her down the bank to the stream and then raped her, the court heard.
The victim said: “I got my phone out to call and say I’ll be home in a minute and that’s when someone ran up to me and grabbed me.
“I was worried that I didn’t have enough oxygen and I might die.
“He was doing it tighter and tighter. I couldn’t speak because my mouth was really swollen.
“At first I tried pretending like I died or something – I flopped down and I had my eyes shut – I though at that point he might have just left – but then I really did fade away.”
The girl described calling out for help – even shouting for one of her teachers – until a passerby heard her calls and came to the rescue.
Anna Vigars QC, prosecuting, said the boy got home late “sweating profusely” and claimed he had fallen off his back.
The court heard his family noticed his “unusual behaviour” over dinner and after hearing about the incident the following day they examined his muddy clothes before calling the police.
Forensic examinations found the boy’s DNA on the victims’ genitalia and underwear, as well as her DNA on him.
Richard Smith QC, defending, told the jury the boy “accepts he has done wrong and serious wrong, by his own pleas – two guilty of the five.”
Describing the defendant, he said: “He’s a 16 year-old who was in mainstream education but, as you’ll hear, was diagnosed as autistic. He is living with a foster family and he has issues in his background.”
Smith said the boy’s intention in grabbing the girl was to sexually touch her, not rape her, and DNA evidence on her clothes and body was a result of him masturbating before leaving school.
He also claimed the girl had “inadvertently” become unconscious after he tripped and fell while leading her away from the path.
The defence went on to describe how, once the boy had sexually assaulted her, he “checked her pulse, went away and watched her come round before fleeing the scene”.
He pleaded not guilty to one charge of attempted murder, one charge of choking the girl with the intent to commit rape and one charge of rape of a child under 13.
The boy admits two counts; that he did take hold of her in an attempt to choke her but the intent was to sexually assault her rather than rape, which he denies.
The trial continues.