A magnitude 6.2 earthquake rocked Afghanistan and various parts of Pakistan on Wednesday, sending people racing out of buildings in the two capitals and injuring at least 13 people and damaging dozens of homes in both countries.

The quake struck at 1041 GMT near Afghanistan's border with Tajikistan in the Hindu Kush mountains at a depth of 111 kilometres, the US Geological Survey said.

Omer Mohammadi, a spokesman for Afghanistan's disaster management authority, said two small children were injured when their home collapsed and one of them was listed in critical condition.

Abdul Razak Zinda, a senior official at a disaster management agency, said 45 houses were damaged in three districts in the northeastern Takhar province of Afghanistan. He said three people were injured.

In Islamabad and Kabul, people fled their offices and homes and recited verses from the Holy Quran in the streets. AFP correspondents in the capital Kabul felt the ground move for at least a minute in the second quake that came a few hours after the first.

In Peshawar, people rushed into the streets following the tremor, fearing aftershocks, witnesses told AFP.

Earlier on Wednesday, a magnitude 5.1 earthquake rattled parts of western Pakistan, near the border with Afghanistan. That quake caused a stampede at a school in Bannu, injuring at least 10 students, according to Mohammad Aslam, a local police official.

Taimoor Khan, a senior official at the provincial disaster management authority in Peshawar, said the quake did not cause damages to buildings, but they were still waiting for the final report from remote areas near Afghanistan.

Afghanistan is frequently hit by earthquakes, especially in the Hindu Kush near the junction of the Eurasian and Indian tectonic plates.

Aid agencies have stressed the need for greater disaster preparedness in the war-torn country, which remains extremely susceptible to natural disasters such as floods, quakes and landslides.

A devastating 7.5-magnitude quake that struck Badakhshan in October 2015 triggered landslides and flattened buildings, killing more than 380 people across the region including 248 in Pakistan.

Earlier Wednesday, a magnitude 5.1 earthquake rattled parts of western Pakistan, near the border with Afghanistan. That quake caused a stampede at a school in Bannu, injuring at least 10 students, according to Mohammad Aslam, a local police official.