The pre-dawn strike took place well inside Pakistan territory, more than 50 kilometres from the Afghan border in Mamuzai village of Kurram tribal district.
Pakistani government officials said it was carried out by a US drone. The US embassy in Islamabad declined to comment.
A senior government official in Kurram told AFP that the drone fired one missile at a two-room compound, killing the commander and destroying the building.
"Resultantly one individual, namely Nasir Mehmood alias Ihsanullah Khurya, s/o (son of) Aqeel Muhammad, was killed," the official said, describing him as an Afghan national and a "mid-level commander of the Haqqani Network".
"The US drone remained in the air even after the strike and was flying there for almost 15 minutes," the official said.
Two Pakistani intelligence officials in the area also said the US had carried out a drone strike, but according to their information the drone fired two missiles and killed two terrorists of the Haqqani network in the compound.
A source close to the Haqqani group confirmed that at least one mid-level Afghan commander had been killed.
The US and Afghanistan have long accused Pakistan of ignoring or even collaborating with groups that attack Afghanistan from havens along the porous border between the two countries, a claim Islamabad denies.
On Sunday the Afghan interior ministry blamed the group for an hours-long attack on Kabul's Intercontinental Hotel in which at least 22 people were killed, including US, Ukrainian, Kazakh and German citizens.
The Taliban has claimed responsibility for the attack through an official spokesman, and authorities are still investigating how the terrorists breached security at the hotel.
This month Washington froze aid to Pakistan worth almost two billion dollars in a move designed to force its military and intelligence apparatus to cut support for Islamist groups.
It also ignited speculation that the US could resume drone strikes or launch operations along Pakistan's border with Afghanistan, where terrorist groups once operated with impunity.
Following the aid freeze, the Pakistani military released a statement citing US Central Command chief General Joseph Votel as assuring them that Washington "is not contemplating any unilateral action" inside Pakistan.
The freeze has cooled the relationship between the uneasy allies and prompted indignation in Pakistan, which insists the US does not recognise the thousands of lives it has lost and billions it has spent in its long battle with extremism.