Turkish television reports said boat shuttles ferried 3,000 pilgrims, most of them from Turkey but some from Armenia and Europe, to Akdamar, in eastern Turkey.
The mass in the renovated church was the second mass held in the Church of the Holy Cross on Akdamar Island on Lake Van since it was renovated in 2005-2007 and turned into a museum. A first mass was held there last year.
A new lakeside pier was built this year to accommodate the faithful, local authorities said.
Nearly 30,000 tourists flocked to the church, which hosts one religious service annually, last year, the Turkish tourism ministry said.
Monsignor Aram Atessian, who the interim head of the Armenian patriarchate who chaired the ceremony this year, told the Anatolia news agency that around 3,000 people arrived on the island, and only 60 percent of them were able to enter the church. The others heard the mass outside through loudspeakers.
The Church of the Holy Cross is one of the rare vestiges of what was once a large Armenian community in Turkey under the Ottoman rule.
Armenians say up to 1.5 million of their kin fell victim to genocide during World War I under the Ottoman Empire.
Turkey counters that 300,000 to 500,000 Armenians and at least as many Turks died in civil strife when Armenians rose up against their Ottoman rulers and sided with invading Russian forces.
In 2009, Ankara and Yerevan signed landmark accords to end decades of animosity establish diplomatic relations and reopen the border, but the effort faltered and Armenia froze the ratification process of the accords.