The tremor was very deep, 194km, and its epicentre was in the Hindu Kush mountain range, near the remote northern Afghan province of Badakhshan.
A 13-year old girl died when a wall in her home collapsed on her and 34 people were injured in the northern Pakistani district of Swat, police officer Shafiullah Gandapur told Reuters.
Disaster authorities in Afghanistan said they did not have any immediate reports of casualties.
Authorities and aid workers said very strong shaking was felt in Badakhshan and across other northern areas.
A spokesperson for the Red Cross said they had no immediate reports of damage from Badakhshan's capital but were making checks on other areas.
Mahzudeen Ahmadi, the head of Badakhshan's information department told Reuters they were also checking the province for any casualties, but had no reports yet.
"We felt a strong earthquake, according to primary information the main place (affected) was Yamgan District," he said.
Some of mountainous Badakhshan's remote villages can be difficult to reach and do not have access to phones or the internet.
In the provincial capital Faizabad, 29-year old Ashraf Nael said he was at home on Tuesday evening when the windows of his family home began rattling strongly for about a minute.
"My brothers and sisters all ran outside... we live in a concrete house, those houses which are made from mud might have been damaged," he said.
In northern Pakistan's Khyber Pakhtunkhwa province, a 90-metre-long wall around a police station collapsed, according to a police district spokesman, but did not cause any casualties.
Shaking could be felt as far away as the Indian capital New Delhi.
In Muzaffarabad, the capital of Pakistan-controlled Kashmir - the site of a deadly earthquake in 2005 in which more than 80,000 people were killed - people ran out of their homes, crying and reciting holy verses, according to a Reuters witness.
Shaking was felt over an area 1000 kilometres wide by approximately 285 million people in Pakistan, India, Uzbekistan, Tajikistan, Kazakhstan, Kyrgyzstan, Afghanistan and Turkmenistan, according to the EMSC.
Large parts of South Asia are seismically active because a tectonic plate known as the Indian plate is pushing north into the Eurasian plate.
