According to National Disaster Management Authority (NDMA), the epicentre of the quake was 23 km north-east of capital Islamabad and it was 10 km deep.
Two women and a nine-year old boy were killed when their house collapsed due to the earthquake in the outskirts of northwestern town of Abbottabad, police said.
The quake, which hit at 1:59 am local time, was felt in several districts. The United States Geological Survey measured the quake at 5.1-magnitude.
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Pakistan faces frequent earthquakes as it is located in an active seismic zone. A powerful quake of 7.6-magnitude in 2005 killed over 74,000 people in the country.