The killings took place in a remote and mountainous area about 160km (100 miles) north of the capital Islamabad as the bus was travelling from the city of Rawalpindi to the city of Gilgit.
Sectarian violence has killed hundreds of Pakistanis in recent years.
Most attacks are in the Northern Areas and in Balochistan province.
Officials say that those killed in the latest attack - in the district of Mansehra - were either shot or beheaded.
"Ten to 12 people wearing army uniform stopped the bus and forced some people off the bus," Mansehra administration chief Khalid Omarzai told the AFP news agency.
"After checking their papers, they opened fire and at least 20 people are reported to have been killed. This is initial information and the final toll may go up. They are all Shias," he said.
Police told AFP that the gunmen were masked, but said the victims were pulled from three separate vehicles in the district, which neighbours the Swat valley, a Taliban stronghold.
"They stopped three vehicles, searched them and picked up people in three batches of five, six and nine and shot them dead. They were all Shias," the police spokesman said.
Sources also claim that five sunnis were also shot deat when they opposed and resisted the bloodshed of shia muslims.
Most of the victims hail from Astore. The dead bodies have been brought to
Shias Targeted
Correspondents say that while Shia-majority Gilgit is a popular tourist destination for wealthy Pakistanis and expatriates, it has suffered from increased sectarian tensions in recent months.
Gigit city is the capital of Pakistan's far northern Gilgit-Baltistan region, and is seen as a gateway to the Karakoram and Himalayan mountain ranges.
Shias and other minority communities say those behind the violence - such as the banned Sunni militant organisation Lashkar-e-Jhangvi and a local outfit Tehreek-e-Ahl-e-Sunnat wal Jamaat- are rarely caught or punished.
Sunni extremists allied to or inspired by al-Qaeda and the Taliban routinely attack government and security targets in northern Pakistan, in addition to religious minorities and other Muslim sects they consider to be infidels.
In February gunmen killed at least 18 Shia bus passengers in a sectarian attack in the northern district of Kohistan.
And in September, Lashkar-e-Jhangvi gunmen stopped a bus and killed 26 Shia pilgrims travelling on a bus in Balochistan province. The attackers were reported to have checked the identity cards of all the passengers before removing the Shias and shooting them.
On April 3, a Sunni Muslim mob dragged nine Shiite Muslims from buses and also shot them dead in the town of Chilas, about 60 miles south of Gilgit.
Mourning and protests
Hundreds of people gathered at Khomar, Gilgit to protests against the mass killing of shias muslims in Mansehra. The protesters blocked the main road at Khomar and chanted slogan against the terrorists and law enforcement agencies. They demanded to arrest the terrorists and bring them to justice. They also demanaded to ensure the safety and security of the passengers travelling between Gilgit and Rawalpindi.
Meanwhile, the shia organizations Majlis-e-Wahdat-e-Muslimin, Shia Ulema Council and Imamia Students Organization have announce 10 day mourning over the killing of Shia muslims in Mansehra.
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