Sara Sharif's body was found on the bottom bed of a bunk, under a blanket and with two handwritten notes tucked under her pillow, a UK court heard.
The details about how the 10-year-old's body was discovered emerged as her father, stepmother and uncle appeared in court charged with the girl's murder.
The trio were arrested at Gatwick Airport in London after they were deported from Pakistan, following an intensive manhunt lasting more than a month.
Schoolgirl Sara was found dead with extensive injuries at her home in Woking, south-west of London, on August 10.
Sara's father, Urfan Sharif, aged 41, her 29-year-old stepmum Beinash Batool and uncle Faisal Malik are charged with murder and causing or allowing the death of a child.
The trio appeared for a brief hearing at Guildford Magistrates' Court near Woking, speaking only to confirm their names, dates of birth and addresses.
They were not asked to enter pleas, but their lawyers said they deny the charges.
They were ordered detained until their next court hearing on Tuesday (local time).
They had flown out to Pakistan one day before Sara's body was found, also taking five of her siblings with them.
Urfan Sharif called police in the UK after he landed in Islamabad to tell them his daughter could be found in the family home.
Police rushed to the two-level red brick property and their search led to an upstairs bedroom with bunk beds.
When police pulled the blanket back they found Sara lying fully clothed, face up, and with her hands placed on her chest, the court heard.
Two handwritten notes were found tucked under the pillows her head lay on, the court heard.
"The actual cause of death has yet to be established," Prosecutor Amanda Burrows told the court.
"But what has been established is the presence of healed fractures and injuries that clearly demonstrated that this child was subjected to multiple events of violence and those incidents of violence had continued over sustained periods of time," she said.
"It also concluded the child died as a result of third-party involvement."
The three suspects had travelled to Islamabad, the Pakistani capital along with five children, a day before police discovered the girl's body.
Police began a search and detained 10 relatives of Urfan Sharif, including his father, brothers and cousins, for interrogation in an attempt to pressure the couple to surrender.
The three suspects were arrested by police in Pakistan last week and put on a flight to Gatwick Airport, where they were arrested.
Sara's five siblings, ranging in age from 1 to 13, were recovered by Pakistani police on Monday evening (local time) from Urfan Sharif's family home in central Pakistan.
A court ordered the children to be placed in the custody of the Child Protection Bureau in Rawalpindi city, close to Islamabad.
– Reported with Associated Press