Local Urdu TV channel Capital said that the strike took place at about 11.45 p.m. (local time) when unmanned U.S. aircraft fired two missiles in the Mir Ali area of North Waziristan, a militancy- plagued region bordering Afghanistan.
One missile hit a motorbike carrying two suspected militants, leaving two riders killed right on the spot, said the report, adding that another missile hit a house suspected of being a militant hideout.
At least one was killed as the house was hit by the missile, reported local media.
More casualties are feared, they said.
The identities of the three killed are not immediately known.
Saturday night's U.S. drone strike is the 16th of its kind in Pakistan this year. Since 2013, at least 100 people have been killed in such strikes, according to Xinhua tally.
Despite the repeated protests lodged by the new government led by Nawaz Sharif, the U.S. has never stopped its drone strikes in Pakistan's northwest tribal regions.
A total of three such strikes have been carried out by the U.S. in Pakistan since Nawaz Sharif took office as the new prime minister of the country last month.