Police have sealed off the charity’s offices in Islamabad and foreign staff given 15 days to leave the country.
Save the Children said it “strongly objected” to the action.
Pakistan has previously linked Save the Children to the fake vaccination program used by the CIA to track down Osama bin Laden.
Save the Children has always denied being involved with the CIA or Pakistani doctor Shakil Afridi, who carried out the program.
The NGO has no foreign staff in Pakistan as they were forced to leave after the accusations emerged in 2012.
Save the Children now has 1,200 Pakistani staff working on projects in health, education and food, the charity said.
The charity, which has operations all over the world, has worked in Pakistan for more than 30 years.
The Pakistani government has not given a formal announcement explaining the decision.
However, one official told the AFP news agency: “Their activities were being monitored since a long time. They were doing something which was against Pakistan’s interest.”
A police official said that Save the Children’s phone calls and offices had been placed under surveillance. Speaking to the Reuters news agency, he added that the charity’s activities were “very suspicious”.
Condemning the move, Save the Children said it was “raising our serious concerns at the highest levels”, adding that its workers were all Pakistani nationals.
A Save the Children official told Reuters that the Pakistan government had been stopping aid shipments entering the country, “blocking aid to millions of children and their families”.
It comes after the Pakistani government announced it was tightening the rules for NGOs, revoking several of their licenses.
Meanwhile, the Norwegian Refugee Council has ceased all operations in Pakistan as its license has not yet been renewed.
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