The name of the town literally means "olives" in Maltese; it derives from the large olive groves that stood in and around the current location of the church and the centre of the town. The town was bestowed with the title of Città Rohan by Grandmaster Emmanuel de Rohan-Polduc in 1777. As was the custom in such events, the people of Ħaż-Żebbuġ built an archway at the entrance to their hometown by way of marking the incipiency of its status as a city. The gateway, known by the locals as "Il-Bieb il-Ġdid" or New Gateway still stands today.
In 1380 a church dedicated to St. Philip of Agira was built in Casal Zebugi, a tract of land situated in the middle of the small communities which had developed during the previous Arab occupation of Malta, namely Ħal Dwin, Ħal Muxi and Ħal Mula and which were eventually joined together forming the village known till today as Ħaż-Żebbuġ. The parish church, designed by Tumas Dingli, was erected in the late seventeenth century instead of an older church. The statue of St. Philip, by sculptor Luigi Fontana, was created in 1864.
Malta is very rich in archaeological remains and Żebbuġ is no exception. It gave its name to an era of prehistoric time when pottery of a kind not known as yet was found in tombs in the area known as Ta' Trapna. Later archaeological finds constructed at around the same time where subsequently known as "Żebbuġ phase" remains. A scattering of Punic and Phoenician tombs were also found together with a small number of cart ruts and other remains.