The girls had spent the past month in hiding amid fears of a crackdown on women's rights by the Taliban.
Members of the women's side flew out of Kabul last month but the youth team were reportedly left stranded as they lacked passports and other documents.
Thirty-two players and their families won visas after the charity "Football for Peace" lobbied Pakistan.
An official with Pakistan's Football Federation said the group, totalling 81 people, would be housed at the federation's headquarters in the eastern city of Lahore. A further 34 people will arrive on Thursday he said.
The players will remain in Pakistan under tight security for 30 days before applying for asylum in third countries, the official said.