Afghanistan's membership came after formal approval by the WTO ministers in the Kenyan capital Nairobi.
Top Afghan government official Khan Rahmani told the conference it was a "historic" event, and that WTO membership was "part of our strategic objectives to achieve economic stability and peace."
WTO Director General Roberto Azevedo said he was "delighted" to welcome Afghanistan.
Yesterday, Liberia joined the WTO at a similar ceremony at the conference in Nairobi, which wraps up tomorrow.