The three-day campaign, which started on Saturday, was aimed at administering polio drops to at least 40,000 children in the Jamrud and Landi Kotal towns of the Khyber tribal district.
Health workers in Jamrud, who Friday refused to join the campaign over threats from militants, later took part after the local administration beefed up security.
Pakistan is one of three countries in the world where polio remains endemic, along with Afghanistan and Nigeria.
But efforts to stamp out the crippling disease have been seriously hampered by militant attacks on health workers inoculating children.
Attacks shot up after the Pakistani Taliban banned polio vaccinations in the tribal region of Waziristan in 2012, alleging inoculation was a cover for espionage.
A senior health official from Khyber told AFP on condition of anonymity: "We may extend the campaign for up to six days because it has been very successful."
But the official said the campaign, which has so far covered at least 60 percent of the area in the two towns, could not be carried out in Bara, the third main town of Khyber, due to security threats.
More than 300 teams had been formed to work on the campaign, said the official, adding that in addition to local health workers, tribal police and volunteers were also taking part.
The campaign was also run on the outskirts of Tirah valley, which saw a concerted military push last year with armed forces targeting Lashkar-e-Islam militia fighters.
According to the World Health Organization, Pakistan recorded 85 cases of polio last year compared with 58 in 2012.