As panicked parents and relatives thronged the school site to search for their loved ones, rescue workers spent hours pulling children from the rubble of the privately run Al-Khair Education Centre.
Most of the victims were under the age of 13 and from low-income households.
At least 45 children suffered injuries, ranging from minor wounds to severe trauma, said Arif Khattak, regional director of the Rescue Department.
Television footage showed rescuers clawing through debris with their bare hands and carrying bloodied children to waiting ambulances as residents crowded the narrow alley where the school stood.
A higher-floor roof collapsed onto classrooms below, crumpling two storeys of the building, a rescue official said.
"The fatalities include 12 girl students and a female teacher," Lady Reading Hospital spokesman Mohammad Asim said.
Three children remained in critical condition with head injuries while most of the injured taken to the hospital had been treated and discharged, he added.
The incident took place at 8.48am local time and the rescue operation lasted for four to five hours, Khattak said.
"It was a weak building structure," Peshawar police chief Mian Saeed said.
"Its roof was overloaded with construction on a weak structure, which caused the collapse."
Saeed said the school's owner had been arrested and an investigation launched.
A total of 110 students were attending lessons in three classrooms when the roof caved in.
Distraught relatives accused the school of ignoring concerns about the building's condition and demanded accountability.
"Make an example of them, a lesson for all, so that no one dares open a school just to make money without providing facilities," said Mohammad Zaman, who lost two nephews in the collapse.
The school was located in a poor crowded neighbourhood of Peshawar, capital of Khyber Pakhtunkhwa where Pakistan's president imposed a state of emergency on Sunday saying the provincial government had failed to tackle Islamist militancy from neighbouring Afghanistan, an allegation it denied.
Pakistan spends less than one per cent of its nearly $US450 billion ($A650 billion) GDP on education, leaving many families dependent on low-cost private schools.
Many of them operate from poorly maintained rented buildings with limited oversight, contributing to recurring safety concerns.
In June, at least 14 children died when the roof of a tutoring centre housed in a dilapidated building collapsed in the eastern city of Lahore.
There was no immediate comment from school officials.
Prime Minister Shehbaz Sharif expressed sorrow over the tragedy and offered condolences to the victims' families, his office said.
Jawad Ahmad, whose son and daughter attended the school and survived, said the news left him devastated.
"It felt as if someone had shot me in the chest when I learned that the school building had collapsed," he said.
The province, governed for years by the party of jailed former prime minister Imran Khan, has frequently been at odds with the federal administration.
President Asif Ali Zardari imposed a new governor on the province when he declared the state of emergency on Sunday, sharpening the tensions.
