Police removed the lock placed on the gate of its head office in Islamabad, the global NGO's spokesman Saeed Ahmed told media.
The government sealed the offices of Save the Children earlier this month, alleging that the charity was "working against the interest of the country", and threatened to expel more foreign aid groups for undermining Pakistan's interests.
The move to let the group operate came after hectic consultation and a decision to transfer the control of the NGOs from Ministry of Finance to Ministry of Interior.
Pakistan has toughened its policies towards international aid groups in recent years, accusing them of acting as cover for spying operations.
Officials said the government had come under a lot of pressure from the US which had expressed concern over the crackdown on NGOs, saying Pakistan was only hurting itself by taking action against aid groups.
Meanwhile, Save the Children in a statement welcomed the government's decision and said it would "continue to work as a credible, transparent and accountable partner" of the government of Pakistan.
The group denied having any link with Afridi or the CIA.
