Under the new programme, 1.5 million children under five years of age would be given an oral vaccine in six districts.
The virus has now been cornered to just a few areas in Pakistan, Afghanistan and Nigeria.
Health teams have been repeatedly attacked since the Taliban denounced vaccines as a "Western plot" to sterilise Muslims and imposed a ban on inoculation in June last year.
Accusations that immunisation campaigns are a cover for spies were given credence after it emerged that the US had used a Pakistani doctor to gather intelligence about Osama bin Laden in 2011.
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On September 30, a Pakistani security personnel was injured when an IED blast targeted a polio vaccination team in the restive tribal region near Pakistan-Afghan border.
Earlier this month, a polio vaccination team in Pakistan's Punjab province had to run for their lives after some residents accused them of being CIA spies and set dogs after them.
Jan Baz Khan Afridi, Deputy Director of the Expanded Programme on Immunisation (EPI) in Khyber-Pakthunkhwa said the campaign has started in Bannu, Dera Ismail Khan, Kohat, Lakki Marwat, Peshawar and Tank districts and will continue till Friday.
The teams would also be assisted by volunteers, lady health workers and officials of national building departments.
Afridi said polio cases has seen a significant reduction in Khyber-Pakthunkhwa, with only seven cases reported this year as compared to last year's 27. In 2012, a total of 58 cases was reported in Pakistan, but only 46 cases has so far this year.
Officials said two cases were reported in Punjab, seven from Khyber-Pakthunkhwa, three from Sindh and 34 from tribal areas this year.