The agreement was published on October 4 during a donors conference for Afghanistan in Brussels after Germany said it would make future aid for Afghanistan conditional on Kabul helping to repatriate migrants.
The bloc is considering returning 80,000 Afghan migrants, dpa reported. More than 170,000 Afghan nationals applied for asylum in the EU in 2015, making it the second-largest group behind Syrians.
Under the deal, Kabul is to provide travel documents within four weeks for any Afghan migrant the EU decides to return home, or the EU can issue its own travel documents.
Repatriation operations have in the past been hampered by migrants not having passports, or the authorities in their home countries refusing to recognize their travel documents.
Under the deal, Kabul agreed that migrants can be returned on regular flights or specially chartered planes, with an initial limit of 50 forced returnees per flight.
The EU is to pay the cost of returning migrants and trying to reintegrate them, while the Kabul airport may establish a dedicated terminal for the returnees.