The protesters, holding banners reading "Death to Israel" and "Death to America", burned effigies of Trump as well as American and Israeli flags in the centre of the Afghan capital.
A few dozen tried to reach the heavily-barricaded US embassy, but were quickly pushed back by Afghan security forces well before reaching it.
In the western city of Herat, an AFP correspondent reported some 2,500 protesters staged demonstrations demanding Trump "reconsider his decision".
Some 500 people also gathered in Kunduz, in the north-east of the country, according to an AFP reporter.
Trump's announcement on Jerusalem has been met with an almost universal diplomatic backlash, and prompted a call for a new intifada from the leader of Hamas. There were sporadic clashes between Palestinian protesters and Israeli security forces.
The status of Jerusalem is deeply sensitive for Muslims, and protesters have been taking to the streets in cities across the world following the policy shift.
Trump's decision puts him at odds with the international community, which insists the issue can only be resolved through negotiations.
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