The prehistoric temple in Ix-Xewkija, first recorded by Gann-Frangisk Abela, points to some activity in the area and it is possible that the place was inhabited since very early times. Trial excavations carried out in 1904 by the archaeologist Father Manwel Magri in the fields east of the parish church confirmed that the area was inhabited since Neolithic times.
Around 700 BC, Malta and Gozo were colonized by the Phoenicians and later by their descendents, the Carthaginians. Several Punic objects were discovered in the limits of Ix-Xewkija at Tal-Morob.
The Romans took over in 218 BC at the beginning of the second Punic War, creating Gozo a municipium independent of Malta. The Romans turned the Citadel into their acropolis and a town developed beneath its walls. The Ix-Xewkija area was definitely inhabited in Roman times. The place was probably dominated by a rustic-type Roman villa, a villa intended for agricultural industrial activity, especially oil-pressing
In 535 AD, these islands passed under the dominion of the Byzantines, until in 870 AD, when Aghlabid Arabs attacked Malta and left the archipelago depopulated. Around 1045, a group of Saracens came over from Sicily and recolonized the island. The toponym Ix-Xewkija must have originated soon afterwards. In 1091, Count Roger the Norman established suzerainty over Malta, which later passed into the hands of the Swabians (1194), the Angevins (1266), and the Aragonese (1282). During this time the islands were governed by a series of feudal lords. Their rule was mitigated from around 1350, when Gozo and Malta were incorporated on and off in the royal domain. A local government known as the Universitas Gaudisii was formed to defend local interests.
It was probably an increase in commerce that led to the development of a settlement in the Ix-Xewkija area which was documented in 1487. The name is first recorded as Xeukie, in an act registered by Notary Joannes Sabbara, and refers to the place as an extensive area. However, a constant flow of corsairs entering Il-Mġarr and Il-Mġarr ix-Xini harbours to plunder and enslave rendered the area unsafe.
In 1530, Emperor Charles V donated Malta and Gozo to the Order of Saint John. Initially nothing changed. In 1551, Gozo was virtually depopulated as the entire population of about 5000 was taken into slavery. Later during the Order’s presence, the Citadel was slowly rebuilt and Gozo flourished once again. The fastest growing settlement was again Ix-Xewkija. By 1607, when Garzes tower was built on the promontory overlooking l-Mgarr harbour, it had become more secure. This security was consolidated in 1661 when another tower was built at the entrance of L-Mġarr ix-Xini inlet. This stepped-up security also led to a growth in the population, resulting in Xewkija being declared a parish in 1678. Later, Knight Giovanni Gourgion built a fortified country residence, known as the Gourgion Tower, in the area of the new parish. Completed by 1689 to become the most imposing building of Xewkija, it became a landmark for the next two and a half centuries.
The rule of the Knights of St John ended on 10 June 1798, when the French, under General Bonaparte, occupied Malta and Gozo. The inhabitants of Ix-Xewkija rushed for safety inside Fort Chambray, but conceded defeat because the Knights did not offer any resistance.
During the French administration Xewkija formed part of the so called Municipality of the City of Gozo, that included also the Citadel and Rabat Citta Vittoria, Gharb, and Ta' Sannat. On 2 September, the Maltese and Gozitans rose against the French, who were expelled from Gozo on 28 October 1798.
The British slowly transformed the islands into a fortress colony. The resistance of the British and the Maltese to the Axis bombardments during the Second World War became a legend. Between 1940 and 1942, eighteen shelters were excavated throughout Ix-Xewkija.
Since the Maltese Islands gained Independence in 1964 and were declared a Republic on in 1974, Gozo has been governed like any other part of the Maltese Islands. The executive functions of the central Government are carried out through the Ministry for Gozo, established on 14 May 1987. Since the establishment of Local Councils in 1993, Ix-Xewkija has elected its own local council.
According to the census taken on 26 November 1995, the population of Ix-Xewkija had grown to 3128.