Construction on the complex began in 1417 under Queen Gawharshad, the wife of Timurid ruler Shah Rukh, and ended in the late 1400s with the building of a madrassa by Sultan Husayn Bayqara.

It was seriously damaged in 1885 during the Panjdeh incident, when the British and ruling Emir of Afghanistan demolished most of the complex buildings.

Shah Rukh made Herat the capital of the Timurid Empire in 1405, moving it from Samarkand.

The complex was then commissioned by Timurid Queen Gawhar Shad and construction began in 1417, likely under architect Kavamad-Din of Shiraz who also built a similar madrasa in Khar Gerd.

The complex had two minarets by its eastern façade on either side of the main entrance and the mausoleum in its northwest corner.

Intervention in the 1950s supervised and led by Fikri Saljuqi resulted in drastically changing the appearance of the building, with construction of an entirely new eastern façade and a partly new southern facade, and the hexagonal Mihrab being demolished and replaced with a rectangular one.

[4] The United Nations Educational, Scientific and Cultural Organization (UNESCO) along with Italian architect Andrea Bruno began preliminary conservation and restoration efforts in 1974–75.

While close to finishing the mosque restoration, Herat's March 1979 uprising and the resultant suppression caused work to end.

At the bottom of the dome, writing in Kufic was partially destroyed on the eastern side and completely gone on the north.

The last minaret that stood at the corners of the mosque was almost completely destroyed by Soviet heavy artillery during this period, leaving only 12 m (39 ft) of its base remaining.

DACAAR added masonry and covered the dome of the mausoleum along with the base with a thin layer of cement.

[7][11][12][13] In 2014, UNESCO and the Afghanistan government coordinated to attempt to preserve and replicate the tile work on the exterior dome.

Mujahedeen fighters launched attacks against the troops stationed there and the Soviet forces laid anti-personnel mines around the base of the minarets.

In 2020, the Aga Khan Development Network made a pledge to the President of Afghanistan to restore a minaret in danger of collapsing.

[27] Nine towers survived the events of 1885, but the explosions had weakened them structurally, and they remained neglected over the next few years due to an unsettled political situation.

No repairs or restorations were undertaken, and over time, four more towers collapsed due to structural weaknesses, earthquake and sheer decrepitude.

Robert Byron wrote it "was as if one saw the sky through a net of shining hair planted suddenly with flowers".

Fakhr-ul Madaris, a religious school with 350 students, was built at its base around 1940, incorporating the minaret into its northern façade.

[5][6] The middle minaret with a height of 42.40 m (139 ft 1 in) has two balconies and was decorated with blue lozenges separated by regular bricks with flower mosaics.

[5][6][1] The mausoleum was originally constructed to house the remains of Prince Baysunghur, a son of the Timurid ruler Shah Rukh and Gawhar Shad.

More distantly related Timurids, Ahmad and Shah Rukh (sons of Abu Sa'id Mirza, who was responsible for Gawhar Shad's execution), were also buried in the mausoleum.

The inner dome is adorned with gold leaf, lapis lazuli and other colours which form intricate patterns.

[28] Lying in the center of the room, they are oblong shaped and made of matt black stone, with floral patterns carved on them.