The mosque was damaged in World War II, and it was subsequently repaired, although the reconstruction was not completely faithful to its original design.

The Sidi Darghut Mosque was built in c. 1560 by the Ottoman governor Dragut, shortly after the 1551 recapture of Tripoli from the Knights Hospitaller.

[1] After Dragut was killed whilst attacking the Hospitallers in the Great Siege of Malta in 1565, his body was taken to Tripoli and buried in the mosque.

[2] A number of alterations were carried out to the mosque by Iskander Pasha in the early 1600s, including the remodelling of the minaret[1] and the construction of a hammam[3] (or at least the renovation of an existing one).

Reconstruction works were undertaken by Ali Mohamed Abu Zaian, and the rebuilt mosque contains a number of differences from the original building.