The Surp Garabed Church is believed to have been built shortly before 1593, as identified from a manuscript. According to tradition, the church was constructed with the help of craftsmen from Van and Muş who had come to Üsküdar for the construction of a mosque. In 1617, the building was renovated through the efforts of Father Zakarya from Van. The church underwent its third restoration in 1727, during the patriarchate of Hovhannes IX Golod, under the direction of the architect Sarkis Kalfa.
Opposite the church stood a monastery built for the clergy of Jerusalem. Patriarch Krikor Shghtayagir of Jerusalem later added new sections to this building. In the following years, it was demolished, and in 1838 the Cemaran School was built to the east of the church. Next to it, there was a large vineyard enclosed by walls.
The church was renovated again in 1844, during the time of Patriarch Asdvadzadur II, but was destroyed by fire in 1887. In 1888, it was rebuilt in stone during the patriarchate of Harutyun I, with the benefaction of the brothers Madteos and Apig Unciyan. On both the right and left sides of its front façade stand two tall stone bell towers.
In its courtyard, the church has three fountains and five gates. Above the entrance courtyard lies a two-story gallery. On either side of the front section are chapels. During the 18th and 19th centuries, this neighborhood became an important cultural center. Patriarch Golod had opened the first school in Istanbul next to the Surp Garabed Church.
The most recent restoration took place in 2006, after which the church was re-consecrated and reopened for worship by Patriarch Mesrob II.