The military has been fighting militants led by a pro-Taliban cleric in the scenic area since October. The clashes have prevented inoculation teams from reaching children in some parts of the valley.
Officials said the girl, Tanzeela, a resident of insurgency-hit Kabal, has the crippling polio virus.
"I can confirm that one polio virus type P1 case has been found in Kabal," Waheed Khan, deputy director of Expanded Programme on Immunisation, told AFP.
Khan said preliminary reports revealed Tanzeela was born in the southern port city of Karachi and that more details were being gathered about the case.
"Special surveillance teams are ready to go into Swat and assess the situation, after which vaccinations will be started in all areas," Khan said.
The number of total polio cases in Pakistan this year is now 16, said officials with the Expanded Program on Immunisation.
Four of those cases were in North West Frontier province, where Swat is located, they said.
The government in May signed a peace deal with militants under which the militants agreed not to block polio vaccination drives and other health initiatives aimed at preventing the spread of measles and tuberculosis.
"But the local authorities have refused to carry out vaccinations for security reasons," another health official requesting anonymity told AFP.
Some 110,000 children live in militant strongholds in Swat that have remained inaccessible, he said.
The World Health Organisation recently listed Nigeria, India, Pakistan and Afghanistan as the only polio-endemic countries in the world.