Their participation was stopped in December 2012 over threat to their lives from Islamist militants, who see anti- polio drive as a sinister conspiracy to sterilise Muslims.
The militant groups have often attacked health workers in Pakistan's restive tribal areas.
However, the bold decision to allow women health workers take party in anti-polio drive in Bajaur Agency near the Afghan-Pakistan border was taken at a meeting three months ago, said Himayatullah, in-charge of the anti-polio campaign.
Extraordinary security measures have been taken for the safety of the women, authorities said.