Previously, one case was reported each in northeastern Punjab province and northern Gilgit-Baltistan, Health Ministry spokesman Saeed Ahmed Shah told Anadolu Agency.
In the recent case, the crippling virus paralyzed an 18-month-old boy in Chaman town of Killa Abdullah district near Afghan border.
The child -- identified as Ahmed Shah -- had only received two to three doses of polio vaccine as his mother and grandmother refused to get the child vaccinated any further, Ahmed said while calling it the main reason behind the case.
The health official said Killa Abdullah, Pashin and Quetta districts are among the most sensitive areas of the country, where polio virus is still active.
Pakistan has already announced to launch a three-day anti-polio campaign starting from July 10 to save millions of children in the country from the life-long crippling virus.
The new anti-polio campaign in Pakistan would be carried out in two phases; the first phase will cover the capital Islamabad, Rawalpindi city, northwestern Khyber Pakhtunkhwa province, Federally Administered Tribal Areas, Gilgit-Baltistan and Azad Jammu and Kashmir.
The second phase will be between July 17 and July 20 in high-risk polio districts of Sindh, Punjab and Balochistan provinces.
"We will vaccinate 10.44 million children under the age of five during this campaign in 73 districts. Around 75,000 workers would take part in this campaign to administer anti-polio vaccine to children," Ministry of National Health Secretary Muhammad Ayub Sheikh told Anadolu Agency on Monday.
He said Pakistan had been very successful in the fight against polio, bringing the cases down from 306 in 2014 to 54 in 2015, and then 20 in 2016.
Pakistan is among three countries in the world, including Afghanistan and Nigeria, where polio virus still exists and the country remains under a polio-linked travel restriction imposed by the World Health Organization (WHO).
In 2014, WHO made it mandatory for all people traveling from Pakistan to carry a polio vaccination certificate.
Armed assailants belonging to militant groups have frequently targeted polio vaccinators and their security detail in several parts of Pakistan. The groups see the anti-polio campaigns are part of an elaborate anti-Muslim and Western conspiracy, and often issue death threats to vaccinators, many of whom are women, for administrating the vital vaccines to children.
In April 2016, assailants gunned down seven policemen who were providing security to polio vaccinators in the southern port city of Karachi.
A doctor involved in the anti-polio campaign in Khyber Pakhtunkhwa province, who wished to stay anonymous due to security concerns, said an estimated 80 people associated with the drive have been killed across Pakistan since December 2012.