Ian Huntley has admitted he killed Jessica Chapman by suffocating her.
Mr Huntley is into a second day of questioning
The former school caretaker, 29, told the Old Bailey he put his hand over the 10-year-old's mouth to stop her screams, but she stopped breathing.
He said her friend Holly Wells had drowned by accident in his bath after the two girls entered his house to tend to Holly's nosebleed last August.
Mr Huntley denies murdering the two girls in Soham, Cambridgeshire, but admits he dumped the bodies in Suffolk.
Richard Latham QC, prosecuting, asked him about him checking Jessica for signs of
life after holding his hand over her mouth.
He said: "You realised you had killed her?"
Mr Huntley replied: "Yes."
After the lawyer asked directly if he had killed her, Mr Huntley whispered: "Yes."
He insisted he did not know how stopping her screaming led to
her being suffocated and said: "I didn't deliberately intend to kill her."
Mr Latham alleged Mr Huntley was holding Holly under the water and that was why Jessica was screaming.
Mr Huntley described putting the bodies into his car and admitted it was a "cold and ruthless" act.
The barrister said he had been acting in a calculated and callous way.
"You were thinking with clinical care, it was like a military operation," he said.
The barrister said Mr Huntley was thinking clearly enough to cut the clothes off to burn them because they contained carpet fibres.
Mr Huntley admits one charge of conspiring to pervert the course of justice and his former girlfriend Maxine Carr denies helping an offender and conspiring to pervert the course of justice.
The morning after the girls died, he spoke to Ms Carr for five minutes and then knocked on his neighbours' doors.
Mr Latham suggested this was to check if anyone was going to say something that would cause a problem with his own story.
That afternoon, he tried to clean a bloodspot on his bed from Holly's nosebleed, Mr Huntley told the court.
Explaining how his bath became cracked, Mr Huntley said he had lost his footing in the bath, but the barrister questioned how this damage could have occurred from bare feet.
Mr Latham said Mr Huntley had been changing his story even during the course of the trial.
But Mr Huntley said his memory has been improving since the summer, following a period of memory loss dating back to the girls' deaths.
Earlier, Mr Latham called the nosebleed story "rubbish" and said Mr Huntley had told a string of "bare-faced lies" to police to cover up what he had done.
At the start of a tense exchange, Mr Latham said: "Jessica was screaming because you were murdering Holly. That is the truth".
Mr Huntley's voice began to raise as he denied this.
Twice, Mr Latham said: "You have just lost your temper with me, haven't you?"
Mr Huntley replied: "Yes."
Mr Latham said: "Did you lose your temper with one of these girls on that Sunday
Mr Huntley: "I had no reason to lose my temper."
Mr Latham said: "Did you become the assertive individual you became two minutes
Mr Huntley: "No I did not."
The former school caretaker admitted approaching Holly's father, Kevin Wells, soon after the girls disappeared on 4 August, to wish him well was "just inexcusable".
But he denied "playing with the emotions" of the parents.
The barrister suggested temptation had been put before him when the girls arrived on his doorstep.
Mr Huntley denied luring the girls into his house by pretending Ms Carr, who was a classroom assistant at the girls' school, was at home.
But he admitted it was "inappropriate" to let Holly into his bedroom while Jessica used
The case continues.