He was appointed as interim chief of the Pakistan Taliban following the killing of Hakimullah Mehsud, the previous leader, in a US drone strike on November 1.
Shaheen’s killers ambushed his car as it passed through Dargah Mandi, a village 5km (3 miles) northwest of Miranshah, the regional capital of North Waziristan.
“Unidentified gunmen in another car shot and killed Shaheen as well as the driver and guards,” a family member told Reuters.
Security sources also confirmed the deaths.
The Pakistani Taliban insurgency is fighting to topple Prime Minister Nawaz Sharif’s democratically elected government and impose Sharia law in the nuclear-armed nation.
Attacks have been on the rise since Sharif came to power in May, promising a negotiated end to violence. His stance unnerved global powers already worried that withdrawal of most US-led troops from Afghanistan in 2014 would leave a security vaccuum.
Peace talks between the Pakistani government and Taliban insurgents began on February 6 but broke down last week after insurgents said they executed 23 men from a government paramilitary force in revenge for the killing of their fighters by army forces.
Shaheen was considered one of the proponents of peace talks, according to sources close to the Taliban.
The failure to reach a negotiated settlement has raised the spectre of a major military offensive in North Waziristan, a region bordering Afghanistan where al-Qaida-linked militants are based.
On Sunday, Pakistani fighter jets attacked suspected militant hideouts in tribal areas on the Afghan border. The army said they killed at least 38 insurgents in the third air strike in recent days.
On Saturday, at least nine people were killed in similar strikes in Hangu district. On February 20, 15 suspected militants were killed when army jets bombed the Mir Ali area of North Waziristan.