The protesters marched to the Iranian Embassy carrying banners condemning Tehran's action.
Iran started to expel the refugees on April 21 and has sent back some 25,000, prompting strong protests by the Afghan government.
Iran has said the government plans to send back around 500,000 refugees in a first phase. There are up to 2 million Afghans in Iran.
Also, U.S.-led coalition forces said four suspected militants were killed and seven wounded during an attack on a government building in Afghanistan's eastern province of Khost.
Afghan police battled for two hours a group of attackers at the administration building in Spera, near the Pakistani border late on April 30, before coalition aircraft launched an air strike.
Two Afghan police officers were also wounded in the fighting.
Kabul Mulls Relations Iran
Afghanistan has recently been preoccupied with its relations with Pakistan. But increasingly, ties with Tehran are coming to the fore. more
Between Washington And Tehran
Afghan Foreign Minister Rangin Dadfar Spanta told RFE/RL in May 2006 that his country could help improve relations between Iran and the United States. more