Pakistan temporarily reopened two main crossings that had been closed after a wave of militant attacks.
The Torkham and Chaman crossings were opened for nationals from both countries with valid visas who want to return home.
Pakistan shut the crossings three weeks ago after a wave of suicide bombings that authorities said was linked to Islamic militants based in Afghanistan.
The two countries have long accused each other of ignoring al-Qaida and other militants who operate along the porous, mountainous border.