The programme, which began in 2002 from both Pakistan and Iran, reached the historic figure as the total number of Afghans returning this year from Pakistan with UNHCR assistance surpassed 200,000.
Speaking in Geneva, the United Nations High Commissioner for Refugees, Antonio Guterres said: "This unprecedented number of people returning to their homeland is a testament to the desire of Afghan refugees to participate in the rebuilding of their country,"
In Iran, UNHCR has assisted nearly 800,000 Afghans to repatriate since the programme began, with another 400,000 leaving on their own. So far this year, some 26,000 Afghans have returned from Iran with assistance from the UN refugee agency.
Total repatriations to Afghanistan from Iran and Pakistan now stand at more than 3.7 million people.