Taliban militants closed down some 39 health centres across Zabul Province, depriving more than 65,000 residents of critical health services, provincial officials say.
Vaccination teams from both countries meet at transit points at the Torkham, Kharlachi, Ghulam Khan and Chaman border crossings and share data about child vaccination and registration.
Religious scholars and local residents are demanding that the Taliban stop blocking children's polio vaccinations.
Easing access for Afghan patients traveling across the border for treatment has allowed them to arrive for appointments on time and receive much needed health care.
Tajik doctors treat thousands of Afghan citizens every year on both sides of the border as part of an agreement between the two countries' health ministries.
Over the next two years, 48 midwives and nurses will undergo training to help reduce maternal and child mortality in remote areas.
Afghanistan is among the few countries in the world that have not been able to completely eliminate the polio disease, due mainly to the lack of security and militants' obstruction.
Taliban closed all but five healthcare facilities in the province in an apparent attempt to force the government to pay ransom.
Almost 10 million Afghan children were vaccinated against polio during a three-day campaign in August.
Militancy is the biggest obstacle to health care in Afghanistan and to Pakistan's efforts to help Afghan HIV/AIDS patients.
Women are receiving training to become nurses or midwives, which will help address the shortage in female health workers in Afghanistan.
Pakistan also plans to educate Afghans on HIV transmission and treatment in order to reduce stigma and encourage people to get tested.