Five people died in various remote regions of the northwestern province of Khyber Pakhtunkhwa, the National Disaster Management Authority said in a statement, and at least 20 homes were damaged.
One man was killed in the mountainous northern region of Gilgit-Baltistan when he was hit by falling rocks in the town of Chilas, an official said.
The epicentre of 6.6-magnitude earthquake was in northeast Afghanistan at a depth of 210 kilometres (130 miles) at 2:58 pm (1028 GMT) on Sunday.
It was felt in the Afghan capital Kabul 282 km to the south of the epicentre and in Pakistan’s capital Islamabad, where some residents evacuated apartment blocks after tremors shook ceiling fans and furniture.
In the Indian capital New Delhi, buildings in the centre swayed and the metro train system was halted temporarily.
Tremors were also felt in Dushanbe, the capital of Tajikistan which borders northern Afghanistan.
Last October a 7.5-magnitude quake ripped across Pakistan and Afghanistan, killing almost 400 people and flattening buildings in rugged terrain that impeded relief efforts.