The blast which virtually destroyed the church occurred at around 10 p.m. (2100 GMT) Wednesday in the village of Gornji Livoc, about 40 miles east of Pristina, Maj. Steve Shappell, a military spokesman, said.
An American platoon was based in line of sight from the church, but the building was not among 150 patrimonial sites guarded by the international peacekeepers.
In January, the peacekeepers entrusted U.N. and local police with safeguarding some of the Serb churches and monasteries in the province.
The decision was criticized by Serb political and religious leaders, who argued that it would lead to further destruction of such buildings by ethnic Albanian militants, most of whom are Muslims.
Dozens of Serb Orthodox Christian churches, including some dating back to medieval times, have been destroyed by ethnic Albanians since Yugoslav forces pulled out of Kosovo and NATO deployed its troops in June 1999, following a 78-day bombing campaign against Yugoslavia.
U.N. police sources said that an abandoned Serb house located in the same village was also destroyed in another explosion a few hours later.
No one has been arrested in connection with the incidents, and investigations were underway.