Severely damaged after British bombardment during World War I, the mosque was restored in 1925 by the Supreme Muslim Council.

[5] The Great Mosque is situated in the Daraj Quarter of the Old City in Downtown Gaza at the eastern end of Omar Mukhtar Street, southeast of Palestine Square.

[7] According to tradition, the mosque stands on the site of the Philistine temple dedicated to Dagon—the god of fertility—which Samson toppled in the Book of Judges.

[3] A Christian basilica was built on the site in the 5th Century AD, either during the reign of Eastern Roman Empress Aelia Eudocia,[9][10] or Emperor Marcianus.

[10] The Byzantine church was transformed into a mosque in the 7th century by Omar ibn al-Khattab's generals,[1][4] after the conquest of Roman Palaestina by the Rashidun Caliphate.

[10] The mosque is still alternatively named "al-Omari", in honour of Omar ibn al-Khattab who was caliph during the Muslim conquest of Palestine.

The relief on the column depicted Jewish cultic objects - a menorah, a shofar, a lulav and etrog - surrounded by a decorative wreath, and the inscription read "Hananyah son of Jacob" in both Hebrew and Greek.

The fact that this Jewish symbol was preserved throughout the decades inside the mosque was described as demonstrating "peaceful coexistence" by scholar Ziad Shehada.

[3] Extensive renovations centered on the iwan were undertaken by the governor Sunqur al-Ala'i during the sultanate of Husam ad-Din Lajin between 1297 and 1299.

[4] Some Western travelers in the late 19th century reported that the Great Mosque was the only structure in Gaza worthy of historical or architectural note.

[23][24] The Great Mosque was severely damaged by Allied forces while attacking the Ottoman positions in Gaza during World War I.

[30] The structure of the mosque was heavily damaged, with some sources describing it as destroyed, by Israeli bombardment during the Gaza war.

Some of the columns have been identified as elements of an ancient synagogue, reused as construction material in the Crusader era and still forming part of the mosque.

The nave arcades are carried on cruciform piers with an engaged column on each face, sitting on a raised plinth.

There is a small mihrab in the mosque with an inscription dating from 1663, containing the name of Musa Pasha, a governor of Gaza during Ottoman rule.

A simple cupola springs from the octagonal stone drum and is of light construction similar to most mosques in the Levant.