Fata Orlovic and 13 other family members have been fighting a legal battle to have the church removed since 2000, when she returned to Konjevic Polje in eastern Bosnia, part of the country run by Serbs since the end of the war.
The church was built shortly after Orlovic and her family were expelled from the village, 20 kilometers (12 miles) east of Srebrenica. Bosnian Serb forces killed thousands of Bosnian Muslims, including Orlovic's husband and over 20 other relatives, in the 1995 Srebrenica massacre.
In its ruling on Tuesday, the court sided with members of the Orlovic family, ordering Bosnian authorities to remove the church from their land "within three months" from the date when the judgment becomes final. The court also ruled that Bosnia must pay damages to 14 members of the Orlovic family totaling 31,000 euros ($33,800).