Name Pakoštane there is only since the 16th century, when he gradually loses name Zablaće. Pakoštane is first mentioned as “villa vocata Pachoschiane” – October 15, 1450. Still in 1498, the parish priest mentioned in Zablaće, but already in 1509 (April 17) judge in Pakoštane.
Pakoštane are justified in the first decade of the 15th century. During the Croatian – Hungarian kings settlement called Pakosene. The documents referred to in 1450 recorded Pachoschiane name and year 1503. Pacoschiane. Later he mentions the name Pakošćane, which is based on Čakavian pronunciation. The present name is derived Štokavian.
Pakoštane in the 15th and 16th centuries often killed by the Turks. According to Jelić, area Pakoštana twice devastated at the end of the 15th century – shortly before 1495 and 1499. Next time get hurt in 1521 when they were looted, and the population is either shelter on nearby islands Vrgada and Pašman. However, it is obvious that at least some people quickly back into place, because according to the census Pakoštane along with ablation counter 164 inhabitants. Pakoštane are again suffered at the beginning of the Cyprus war (1570), when they are abandoned by the inhabitants. Zablaće died three years later (1573). Population ablation is largely avoided in Pakoštane, however, it is known that there very briefly suspended. Specifically, Pakoštane updated in 1597, and until then, according to the Zadar prince Michiel “villaggio dishabitato” – unoccupied (abandoned) village.
Pakoštane were feud, which is assigned to the Zadar family Karnarutić 1446 for meritorious incurred Venetian Republic. It is family Karnarutić gave fortificated Pakoštane, or gird village walls. The task was entrusted to twelve families – six from Biograd, four from Zlosela (Pirovac) awards and two from Murter. The right of Pakoštane with family Karnautić (through female lineage) took the family Senjanović from Biograd.
Pakoštane are after fortification developed in the village. The population gradually increased until the beginning of the Candian war. However, it is the general provider Foscolo ordered to demolish Pakoštane, a population prone to nearby islands. The men, able to fight, were sent to reinforce the defense of Biograd.
According to tradition, during the struggle with the Turks, the population sought shelter in the nearby island Babuljas and able to fight the others defend behind the wall.
About Pakoštane in the period from the 15th to the 17th century speaks very few historical sources. The most important sources are in fact the Apostolic Visitor Valier and Priuli and Archbishop Ivan Parzago. Based on their visitations to some extent it is possible to follow the historical events and identify certain landmarks in time. However, they are primarily attention given church situation.
Among the cultural and historical sights in Pakoštane emphasize the church: the church of St. Justin, located on the same island in front of the village, on the island is the old cemetery. It was built in 1794. Church of St. Michael, the old parish church was built in 1694, was located around the cemetery. Uzašašće Gospodinovo, the current parish church, built of stone in 1906 on the site of the old parish church, with St. Justin most recognizable symbol of Pakoštane. The Church of St. Rocco, built in the 18th century, during the communist era was turned into a warehouse.