The organisation's country office in the capital has been sealed and its foreign staff has been directed to leave Pakistan within 15 days, police said.
A statement issued by the Interior Ministry said the international NGO was involved in "anti-Pakistan activities", Geo News reported.
It is not the first occasion when the NGO has been asked to leave Pakistan. In 2012, the charity's expat staff were forced to leave the country after an intelligence report linked it to a fake vaccination programme launched to track down Al Qaeda chief Osama bin Laden.
Save the Children has always denied it had any links with Afridi or the CIA.
The NGO's activities had been under strict scrutiny for the past six months.