The girls were killed when a stampede broke out in their school in Taluqan city, the capital of the remote province of Takhar.
"The students rushed to escape the school building, triggering a stampede," Takhar education department chief Enayat Naweed told AFP.
"Twelve students, all minors, were killed and 35 others were injured."
Separately, in Nangarhar province, bordering Pakistan, Six people were killed and 69 others were injured, Najeeb Kamawal, head of the local public hospital told AFP.
"Some people are trapped under debris in some districts of Nangarhar province," Yousufzai said.
"This is the not the final toll -- it is expected to keep rising."
A powerful 7.5 magnitude quake struck Afghanistan's Hindu Kush region and was felt throughout much of South Asia, killing scores of people, with fears the death toll could rise substantially.
The US Geological Survey put the epicentre near Jurm in Badakhshan province, neighbouring Takhar, at a depth of 213.5 kilometres.
Thousands of frightened people rushed into the streets across Afghanistan, Pakistan and India as the quake rocked a swathe of the subcontinent.
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