The female students were on the 4th floor of their school in the Takhar province, west of the epicenter of the 7.5 quake. As the major tremor was felt they attempted to flee, resulting in a stampede that killed 12 of them and injured 25 others, AFP reported.
Sonatullah Taimor, the spokesman for the Takhar provincial governor, said another 30 girls have been taken to the hospital in the provincial capital of Taluqan.
Pakistani officials said the death toll in their country from the earthquake has risen to 145, bringing the overall total to at least 180.
Buildings were evacuated in the capitals of Pakistan, Afghanistan and India and communications were disrupted in many areas. Five people have died with 55 injured in the eastern Afghan city of Jalabad, according to hospital sources.
The US Geological Survey (USGS) initially said the quake had a preliminary magnitude of 7.7 and was centred 45km south-west of Jarm, Afghanistan, in the mountainous Hindu Kush region. Then, it revised it down to 7.6 and later to 7.5.
Nawaz Sharif, the prime minister of Pakistan, has placed all federal and military agencies on alert following the quake. His Indian counterpart Narendra Modi tweeted that he had ordered an urgent assessment of any damage.
Phone coverage in remote areas of Afghanistan has remained down in the hours after the quake, international aid agencies reported.