Pakistani authorities have given Save the Children 15 days to leave the country, officials said on Friday, accusing the aid agency of spying.
Police locked the gate of the charity's office in the capital Islamabad late on Thursday and put up a notice saying the building was sealed.
"We strongly object to this action and are raising our serious concerns at the highest levels," Save the Children said in a statement.
"All our work is designed and delivered in close collaboration with the government ministries across the country and aims to strengthen public service delivery systems in health, nutrition, education and child welfare."
The charity, which has been in Pakistan for over 35 years, has had run-ins with the government since 2011, when it was linked to Shakil Afridi, a Pakistani doctor recruited by the CIA to help in the hunt that led to the killing of Osama bin Laden in Abbottabad.
Save the Children's foreign staff members were expelled from Pakistan soon after the accusations surfaced, but more than 1,000 local staff have continued to operate. The charity denies any links with the Pakistani doctor or the CIA.
Police sources, speaking on condition of anonymity, said the aid agency was being shut down because it was involved in "anti-Pakistani projects."
"We have been monitoring their calls and watching their offices and their activities are very suspicious," a senior police official said in Islamabad.
An official at the charity said several staff members had been denied visas since 2012, and aid supplies had been blocked by Pakistani authorities.
"These restrictions have blocked aid to millions of children and their families," the official said. "Hopefully better sense will prevail."
Aid workers say Pakistan has toughened its policies towards both international and local groups, accusing them of using their work as a cover for espionage.
Of particular concern is the Foreign Contributions Regulation Act 2015, a bill that, if approved, would make it easier for officials to prevent groups that receive foreign funds from operating in Pakistan.
According to CIVICUS, a global alliance of civil society organisations, the Pakistan government deregistered 3,000 local aid groups in December last year.