Demonstrators marched outside the Iranian embassy accusing Tehran of interfering in Afghanistan’s affairs.
Soaring fuel prices have angered many Afghans at a time of high demand during winter.
Afghan officials say 2,500 fuel tankers are stranded at the border. Iran denies blocking fuel exports to Afghanistan.
It is thought the Iranian government fears the fuel could be used by foreign forces, but Afghan officials say these concerns are unfounded.
Earlier this week Iran’s ambassador in Kabul, Fadahoseyn Malaki, dismissed reports that Iran had barred fuel exports to Afghanistan.
“We give fuel to the Afghan nation,” he told a news conference, although he added his government still had concerns which “should be addressed”.
Friday’s demonstration was led by Afghan MP Najib Kabuli, who has organised similar protests against Iran in the past.