NATO troops known as KFOR fired tear gas and small arms and some protesters fired back with handguns.
Hundreds of Serbs confronted KFOR troops in armored personnel carriers near a barricade just outside the town of Zvečan in a Serb-dominated northern area of Kosovo, pelting them with stones.
"One KFOR soldier has been wounded, has been evacuated and he is stable," said NATO spokesperson in Kosovo Uwe Nowitzki.
"KFOR will respond in self-defense accordingly if that is necessary," he said without giving further details.
Kosovo, 90% ethnic Albanian, declared independence from Serbia in 2008. But Serbs dominate in a small swathe of the north bordering Serbia which continues to function as part of the Serbian state, resisting efforts by the Kosovo government to extend its authority.
Dragiša Milović, the mayor of Zvečan which is about 60 km from the capital Pristina, said KFOR had refused to allow Serb medical personnel to help wounded Serbs.
"A (KFOR) commander told me they have the authority to use deadly force on anyone who throws a stone or uses a weapon," he told Reuters.
Milovic said he had asked Serbs to withdraw and restore calm.
Kosovo Serbs set up barricades along boundary crossings with neighboring Serbia last year, after authorities in Pristina and European Union's police and judiciary mission EULEX attempted to establish their presence there.
A Kosovo policeman was killed in an ambush and several civilians and NATO troops were injured in clashes that erupted over months.
Earlier this year, Belgrade sought to mend ties with Kosovo and agreed to open border crossings and establish cooperation with Pristina on issues like driving licenses, land registration and school diplomas to secure European Union candidacy.
The then pro-Western authorities in Belgrade have blamed nationalists from the four Serb municipalities in Kosovo's north of stirring up trouble ahead of Serbia's May parliamentary and presidential elections, which ended in a victory for rightist Tomislav Nikolić.
Nikolić took an oath of office on Thursday (31 May) and pledged he would maintain Serbia's EU bid, but that he would never renounce Kosovo as an integral part of Serbia.
Independent Kosovo has been recognised by 90 countries, including the United States and 22 of the EU's 27 member states.