The first polio case was detected in the North Waziristan region, also known as the strong bastion of Taliban and Al-Qaeda linked militants, earlier this month, with officials expecting a "bigger outbreak" of the disease.
"This is the second child, a 36-month-old boy getting paralysed after contracting polio," the World Health Organization's senior coordinator for polio eradication in Pakistan, Elias Durry, told AFP.
Tribesmen in North Waziristan had endorsed the Taliban ban and stopped authorities from vaccinating children under a nationwide campaign in June last year.
"The problem is that it is just a tip of the iceberg," Durry said, adding, "this is what will happen if we have children without polio vaccination".
He said: "We fear there will be more cases in North Waziristan, its neighbourhood and other tribal regions and northwestern districts if the vaccine is not administered to the children."
He said there were approximately 161,000 children in North Waziristan district alone who have not been administered with a polio vaccine since June last year.
The Taliban have alleged that the vaccination campaign is a cover for espionage.
Efforts to tackle the highly infectious disease have been hampered over the years by local suspicion about vaccines being a plot to sterilise Muslims, particularly in Pakistan's conservative and poorly educated northwest.
Pakistan, Afghanistan and Nigeria are the only three countries in the world where the highly infectious, crippling disease remains endemic. Infections shot up from a low of 28 in 2005 to almost 200 last year.