The two royal mausolea, located in the cemetery behind the qibla wall of mosque, were rebuilt on their stone bases following the earthquake of 1766/1179 AH. The Mausoleum of Mehmed II is a decagonal building covered by a dome. The corners of the decagon are marked with pilasters on the exterior and the walls are capped with a rococo cornice. Entered through a low vestibule to the northeast, the mausoleum remains as it was restored during the rule of Abdülaziz I (r. 1861-1876.1277-1293 AH). The Mausoleum of Gülbahar Sultan is a hexagonal domed unit and houses the tombs of Gülbahar, the wife of Mehmed II, one of their daughters and two other palace members. In 1817, a third large mausoleum was built in the cemetery for Naksidil Sultan, mother of Mahmud II (r. 1808-1839/1223-1255 AH), in the contemporary empire style. The cemetery, which holds graves of many significant people, was also enclosed at this time. 

Sixteen madrasas, arranged in two rows of four to the northeast and southwest of the mosque area, are called the Black Sea Madrasas (Karadeniz Medreseleri) and Mediterranean Madrasas (Akdeniz Medreseleri). Each madrasa complex is composed of four senior madrasas that abut the mosque precinct and four junior madrasas (tetimme medreseleri) placed behind them. Three of the four junior madrasas on the Black Sea Complex have been rebuilt at different points in time, while the junior madrasas of the Mediterranean complex have been demolished to give way to the expansion of arterial streets in 1928. The Mediterranean madrasas were modified further in 1958 when the walls of the senior madrasas were excavated to match the street level. 

Each senior madrasa has nineteen domed rooms, a large classroom (dersane) and two service iwans protected by a domed arcade enclosing a rectangular courtyard. Their classrooms have mihrab niches and are distinguished with ornamental brickwork on window exteriors. The junior madrasas are of equal length but are lower and less wide than the senior madrasas. They have ten rooms each with a flat-roofed arcade on two or three sides of a long and thin courtyard. The portals of all eight madrasas face the mosque and their arcades have been glazed for contemporary use. 

The hospital (darüşşifa) and the hospice (tabhane) had their own enclosed precincts to the southwest of the mosque and the madrasas. The hospital, no longer extant, was probably destroyed in the 1766/1179 AH earthquake; its site has been taken up by housing. It was built on a square plan, with rooms of various sizes around a courtyard with a domed arcade. 

The hospice has survived to our day with some rebuilding in the 19th century when it was converted to a madrasa. It boasts a rectangular courtyard building with a forecourt to the northwest. It has ten single-bay rooms on all four sides of the arcaded courtyard, double-bay spaces on either end of the northeast and southwest wings and a large domed iwan placed on axis with the entrance at the center of the southeastern wing. The double-bay rooms on the north and west corners are the hospice kitchens and are accessed only through the forecourt. The other two are side iwans that lead into adjoining dining rooms. The large iwan, ornamented with muqarnas pendentives, has stalactite niches on either side of the entrance and on qibla wall. A set of stairs set into a wall on the southwestern wing leads up to a mezzanine (kursunluk) and storage areas; there is a side entry located next to the stairs. The hospice is constructed of stone, except for portions of the southeastern wall, which was restored in brick and stone.

There was once a soup kitchen (imaret) and a caravanserai (han) sited along the southwestern wall of the hospice precinct. Little remains of the soup kitchen; it was a small building with three rooms in a U-shaped plan. It provided food twice daily for the guests in the caravanserai, the students of the madrasas, and employees of the complex as well as the poor people in the neighborhood. There were remains of the caravanserai until 1930, it has since been rebuilt with extensions and is used for commercial purposes. It was a long rectangular building consisting of a series of rooms with barrel vaults. Also found in the hospice precinct is a structure built as a police station (karakolhane) by Mahmud II in 1838 (1254 AH) and another to the south of the hospice that was built as a Military High School in 1875 (1292 AH)

The complex had a library (kütüphane) and a Qur'an School (mekteb) that were single unit structures located along the precinct walls probably between the Painter's Gate and the Pastry Maker's Gate. The library was lost sometime during the 19th century. The current library of the complex was built in 1742/1155 AH by Mahmud I and is located to the southwest of the mosque, adjoining the prayer hall. There is no trace of the Qur'an school.

The complex also had a hamam, called the Karaman or Irgatlar Hamami, located inside the Malta Bazaar (Malta Çarsisi) to the northwest of the complex. It was taken down in 1928. 

Sources:

Ayverdi, Ekrem Hakki. Osmanli mi'marisinde Fatih devri : 855-886 (1451-1481): III, 356-387. Istanbul: Baha Matbaasi, 1973. 

Goodwin, Godfrey. A History of Ottoman Architecture, 121-131. London: Thames and Hudson, 1997. 

Gulgonen, A. and Bilsel, C. Le complexe de Fatih et son role dans la transformation morphologique d'Istanbul. Paris: Ecole d'Architecture Paris-Belville, 1991.

Hafiz Hüseyin Ayvansarayi. The Garden of the Mosques: Hafiz Hafiz Hüseyin al-Ayvansarayi's guide to the Muslim monuments of Ottoman Istanbul. Translated and annotated by Howard Crane, 11-16. Leiden: Brill, 2000. 

Kuran, Aptullah. The Mosque in early Ottoman architecture. Chicago: University of Chicago Press, 1968. 

Oz, Tahsin. Istanbul Camileri. Vol. 1, 56-59. Ankara: Türk Tarih Kurumu Basimevi, 1987.