Kistanje was first mentioned as in 1408. It originated close to the remains of a Roman camp Burnum and medieval church. During the Middle Ages it was part of Luka parish and it belonged to Šubić noble family. In 1537 an Orthodox church dedicated to St. Nicholas was built. Kistanje was a trade center of this part of Bukovica. After the Kuridža rebellion in 1704, the village was renamed to "Kvartir"; in the 19th century it was again known as "Kistanje". In 1888, the second Orthodox church, dedicated to Sts Cyril and Methodius was built. In 1894 the Catholic Church of Our Lady of Health was built. In the 19th and the first part of the 20th century, Kistanje was the centre of a municipality that was abolished in the 1960s. The municipality and its territory were joined to the municipality of Knin.