The first Mughal Emperor, Babur, was succeeded by his son, Humayun, who ruled in India for a decade but was expelled. Eventually he took refuge with the Safavid shah of Persia, who helped him regain Delhi in 1555, the year before his death. Humayun's Persian wife, Hamida Begum, supervised the construction from 1562-1572 of her husband's tomb in Delhi. The architect, Mirak Mirza Ghiyuath, was Persian and had previously designed buildings in Herat (now northwest Afghanistan), Bukhara (now Uzbekistan), and elsewhere in India. The location chosen for the building on the bank of the Yamuna river adjoins the shrine of an important Sufi Chistiyya order saint, Nizam al-Din Awliya. The Chistiyya was particularly venerated by the Mughals; Humayun's son, Akbar, would build his new palace at Fatehpur Sikri next to the shrine of another saint of the Chistiyya order.

The tomb established some of the important norms for later Mughal mausolea. It is set in a geometrically arranged garden criscrossed by numerous water channels and probably representing symbolically a paradise setting. Such typical Persian gardens had been introduced into India by Babur; later they would be found in the Red Fort in Delhi and at the Taj Mahal in Agra. The architectural form of the building is Persian and especially in its main chamber shows some familiarity with the tomb of the Mongol Ilkhanid ruler of Persia, Oljeytu, at Sultaniyya. It is one of a long line of Mughal buildings influenced by Timurid architecture, notably the tomb of Timur (Tamerlane) in Samarkand. Babur was proud of his Timurid heritage and deeply regretted his inability to hold Samarkand. His successors continued to dream of regaining Samarkand and would interrogate visitors about Timur's tomb. Humayun's tomb is the first Indian building to use the Persian double dome; it is noteworthy for its harmonious proportions. As with later Mughal tombs, that of Humayun is set upon a podium or platform (see another example in the Taj Mahal). The most obvious Indian features of the architecture are the small kiosks or chhatris on the roof. The building is also noteworthy for its inlaid tile work, carving embodying both Indian and Persian decorative elements, and its carved stone screens.

The Tomb of Isa Khan, located outside the main grounds of Humayun's tomb, was built in 1547. It commemorates an important notable who served Sher Shah, the Afghan ruler of Delhi who had ousted Humayun. The octagonal form of the tomb has a long history in Islamic art and became popular in India in the second half of the fourteenth century for members of ruling families. A possible direct model for Isa Khan's tomb is the tomb of Sikandar Lodi (not shown here), built three decades earlier in Delhi. To the untrained eye, the tomb of Isa Khan has the more graceful proportions. Its particular evocation of the form is noteworthy for the elegant clustering of chhatris (kiosks) and pinnacles around the dome, features which were absent on the Lodi tomb.