Programs to reach every child under the age of 5 are being coordinated with the World Health Organization to reduce the risk of the virus spreading across the border.
WHO is seeking to eliminate polio by next year.
Last year Pakistan had the highest number of polio cases in the world, partly because immunization teams were only made up of male health care workers who were unwelcome in some areas.
Now local women in those areas have been trained to administer the vaccine.
In Afghanistan there remains only one reservoir of the virus in the south of the country.
WHO hopes tackling polio across the whole region simultaneously is the best way of stopping transmission of the paralyzing virus by the end of this year.