The magnitude 6.1 quake was centred in mountainous Hindu Kush region in Afghanistan, at a depth of 210 km (130 miles), the US Geological Survey said.
Officials in Kabul said they were assessing damage in areas around the sparsely populated epicentre.
In Pakistan, tremors shook furniture and power cable poles. There were no immediate reports of casualties.
Waseem Ahmad, spokesman for the National Disaster Management Authority in Islamabad, estimated the quake to be about 6.4 magnitude.
"I was with my kids at a badminton court when we felt strong jolts," said Nusrat Jabeen in Pakistan's capital. "It was very scary. We felt everything was shaking. We ran out for safety."
Tremors were also felt in India's mountainous Kashmir state where people rushed out of their homes and offices.
The Indian subcontinent has suffered some of the largest earthquakes in the world.