The palace complex is located on the Seraglio Point (Sarayburnu, سرای بورونی), a promontory overlooking the Golden Horn, where the Bosphorus Strait meets the Sea of Marmara. The terrain is hilly and the palace itself is located at one of the highest points close to the sea. During Greek and Byzantine times, the acropolis of the ancient Greek city of Byzantion stood here.

After Sultan Mehmed II's conquest of Constantinople (known since 1930 in English as Istanbul) in 1453, the Great Palace of Constantinople was largely in ruins. The Ottoman court was initially set up in the Old Palace (Eski Saray, اسكی سرای), today the site of Istanbul University in Beyazit Square. Mehmed II ordered that construction of Topkapı Palace begin in 1459. According to an account of the contemporary historian Critobulus of Imbros the sultan "took care to summon the very best workmen from everywhere – masons and stonecutters and carpenters ... For he was constructing great edifices which were to be worth seeing and should in every respect vie with the greatest and best of the past." Accounts differ as to when construction of the inner core of the palace started and was finished. Critobulus gives the dates 1459–1465; other sources suggest construction was completed in the late 1460s.

Mehmed II established the basic layout of the palace. His private quarters would be located at the highest point of the promontory. Various buildings and pavilions surrounded the innermost core and winded down the promontory towards the shores of the Bosphorus. The entire complex was surrounded by high walls, some of which date back to the Byzantine acropolis. This basic layout governed the pattern of future renovations and extensions. The layout and appearance of Topkapı Palace was unique amongst not only European travellers, but also Islamic or oriental palaces. European travellers described it as "irregular, asymmetric, non-axial, and [of] un-monumental proportions". Ottomans called it "The Palace of Felicity". A strict, ceremonial, codified daily life ensured imperial seclusion from the rest of world. One of the central tenets was the observation of silence in the inner courtyards. The principle of imperial seclusion is a tradition that was codified by Mehmed II in 1477 and 1481 in the Kanunname Code, which regulated the rank order of court officials, the administrative hierarchy, and protocol matters. This principle of increased seclusion over time was reflected in the construction style and arrangements of various halls and buildings. The architects had to ensure that even within the palace, the sultan and his family could enjoy a maximum of privacy and discretion, making use of grilled windows and building secret passageways.

Later …

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The main street leading to the palace is the Byzantine processional Mese avenue, known today as Divan Yolu ('Council Street'). This street was used for imperial processions during the Byzantine and Ottoman era. It leads directly to the Hagia Sophia and turns northwest towards the palace square to the Fountain of Ahmed III.

The Imperial Gate is the main entrance into the First Courtyard. The sultan would enter the palace through the Imperial Gate (Turkish: Bâb-ı Hümâyûn, meaning 'royal gate' in Persian, or Saltanat Kapısı) located to the south of the palace. This massive gate, originally dating from 1478, is now covered in 19th-century marble. Its central arch leads to a high-domed passage; gilded Ottoman calligraphy adorns the structure at the top, with verses from the Qur'an and tughras of the sultans. The tughras of Mehmed II and Abdulaziz, who renovated the gate, have been identified.

According to old documents, there was a wooden apartment above the gate area until the second half of the 19th century. It was used as a pavilion by Mehmed, a depository for the properties of those who died inside the palace without heirs and the receiving department of the treasury. It has also been used as a vantage point for the ladies of the harem on special occasions.

Surrounded by high walls, the First Courtyard (I. Avlu or Alay Meydanı) functioned as an outer precinct or park and is the largest of all the courtyards of the palace. The steep slopes leading towards the sea had already been terraced under Byzantine rule. Some of the historical structures of the First Courtyard no longer exist. The structures that remain are the former Imperial Mint (Darphane-i Âmire, constructed in 1727), the church of Hagia Irene and various fountains. The Byzantine church of Hagia Irene was used by the Ottomans as a storehouse and imperial armoury. This courtyard was also known as the Court of the Janissaries or the Parade Court. Court officials and janissaries would line the path dressed in their best garb. Visitors entering the palace would follow the path towards the Gate of Salutation and the Second Courtyard of the palace.

The large Gate of Salutation, also known as the Middle Gate (Turkish: Orta Kapı), leads into the palace and the Second Courtyard. This crenellated gate has two large, pointed octagonal towers. Its date of construction is uncertain; the architecture of the towers appears to be of Byzantine influence. An inscription at the door dates this gate to at least 1542. The gate is richly decorated with religious inscriptions and monograms of sultans. Passage through the gate was tightly controlled and all visitors had to dismount, since only the sultan was allowed to enter the gate on horseback. This was also a Byzantine tradition taken from the Chalke Gate of the Great Palace. The Fountain of the Executioner (Cellat Çeşmesi) is where the executioner purportedly washed his hands and sword after a decapitation, though there is disagreement about whether the fountain was actually used for this purpose. It is located on the right side when facing the Gate of Salutation from the First Courtyard.
• The Gate of Salutation, entrance to the Second courtyard of Topkapı Palace
• Tughra of Mahmud II on the Gate of Salutation
• The Imperial Mint of the Ottoman Empire
• Byzantine Church Hagia Irene
• Hagia Irene interior
In April 2021, archaeologists uncovered a Roman period gallery consisting of three sections during the underground researches carried out in Topkapı Palace. The gallery located near the Imperial Gate was revealed during the excavation of the First Courtyard.