The campaign, focusing on children under the age of five, started Monday and will last for five days.
Provinces in the south, east and center of the country will be focused on.
As a result of an agreement between the UN and Taliban members responsible for health earlier this month, thousands of children were vaccinated against the polio virus in Shahwalikot.
UN Humanitarian Coordinator for Afghanistan Toby Lanzer said “In 2017 the district of Shahwalikot in Kandahar province recorded five new polio cases, the highest number in any district in the world”
Lanzer also said the polio virus spreads very quickly, and it was crucial for a series of at least three mass vaccination campaigns to take place to prevent the disease from reaching more children in the area.
Shahwalikot is one of the most insecure regions in the southern Kandahar province.
Meanwhile, Afghanistan Independent Human Rights Commission (AIHRC) has said the practice of preventing children from being inoculated against polio in insecure regions of Afghanistan is concerning.
As polio is incurable so the vaccine is the only way to protect children against it.
Afghanistan, Pakistan and Nigeria are the three countries in the world where polio has not been eradicated completely.