Friday's magnitude 6.1 earthquake was centred in the mountainous Hindu Kush region in Afghanistan, at a depth of 210km (130 miles), the United States Geological Survey said.
There were no immediate reports of casualties.
Officials in the Afghan capital, Kabul, said they were assessing damage in areas around the sparsely populated epicentre.
In Pakistan, tremors were felt as they shook furniture and power cable poles, according to witnesses.
Waseem Ahmad, a spokesman for the National Disaster Management Authority in Islamabad, estimated that it was a 6.4 magnitude earthquake.
"I was with my kids at a badminton court when we felt strong jolts," Nusrat Jabeen told Reuters news agency in Pakistan's capital.
"It was very scary. We felt everything was shaking. We ran out for safety."
Tremors were also felt in Indian-administered Kashmir where people rushed out of their homes and offices.
The Indian subcontinent has suffered some of the largest earthquakes in the world. As per Indian media reports, tremors were felt in the capital New Delhi, Mathura, Lucknow, Prayagraj, occupied Kashmir, and several other parts of North India.
Pakistan is among the most earthquake-prone regions in the world. The country is located on the Eurasian Tectonic Plate, which is known for high levels of seismic activity.
This September, over 40 people were killed and more than 300 injured after a strong earthquake rocked Mirpur in Azad Kashmir.
In October 2005, a massive earthquake killed over 80,000 people in Azad Kashmir and Khyber Pakhtunkhwa.
