It was built with its complex structures (külliye) to the area where ruins of the Holy Apostles Church remained in years between 1463 and 1470, in Sultan Mehmet the Conqueror period.
The mosque was destroyed which cannot be repaired again in an earthquake in 1766. Second Fatih Mosque rebuilt in years between 1767 and 1771 in Mustafa III (1757-1774) period. The architect of the new mosque is Mehmet Tahir Aga who is also the architect of Laleli Mosque. The tile panels decorating two window facade in interior courtyard are actual decorations of the first mosque. Mausoleum of Sultan Mehmet the Conqueror is located in the direction niche.