The Church of Surp Khach, or Holy Cross, was built between 915 and 921 during the reign of Armenian King Gagik I.
The church will function as a museum, not a place of worship, following its $1.5m (£763,000) restoration.
The spiritual leader of Turkey's Armenian community, Patriarch Mesrob II, called for services to be held at least once a year.
The church is situated on an island in Lake Van, known as Akdamar - or Akhtamar in Armenian.
Frescoes of saints adorn the inside of the tower.
Biblical scenes are depicted in carvings on the facade.
Turkey hopes the restoration will help to heal a rift with Armenia. Armenian dignitaries said they hoped many more churches would be restored.