More than 90 centres across Pakistan will register the Afghans and issue them proof of registration cards in the campaign, which ends on December 31, said Vivian Tan, a spokeswoman for the United Nations High Commissioner for Refugees (UNHCR).
There are about 2.5 million Afghans in Pakistan, many of whom arrived after the 1979 military invasion of Afghanistan by the former Soviet Union.
But some Afghans are in Pakistan to find work and escape poverty in their homeland.
Afghans mainly live in dusty refugee camps or in squalid settlements near some major cities across Pakistan.
The National Data and Registration Authority will enroll the Afghans and issue them cards carrying their names, photos, educational qualifications and places of origin, in the first registration scheme since Afghans started arriving in Pakistan, Tan said.
"It will give [the Pakistani government] a clear sense of who is in their country [and] will help the government get a profile of the Afghan population in Pakistan," she said.
UNHCR has provided six million dollars for the Pakistani government programme, she said.
While some left Afghanistan for economic reasons, others left to escape the repressive rule of the Taliban regime, which enforced a strict implementation of Islamic laws under which women were not allowed to work or go to schools and criminal offenders were treated harshly.