Malta is home to what may be the oldest freestanding structure in the world: the oldest of all the megalithic temples on the islands is il-Ġgantija, in Għawdex dating back to before 3500 BC. One of the very earliest marks of civilization on the islands is the temple of Ħaġar Qim, which dates from between 3200 and 2500 BC, stands on a hilltop on the southern edge of the island of Malta. Adjacent to Ħaġar Qim, lies another remarkable temple site, l-Imnajdra. The society that built these structures eventually died out or at any rate disappeared. Phoenicians colonized the islands around 700 BC,^[1] using them as an outpost from which they expanded sea explorations and trade in the Mediterranean.

The islands later came under the control of Carthage (400 BC) and then of Rome (218 BC). The islands prospered under Roman rule, during which time they were considered a Municipium and a Foederata Civitas. Many Roman antiquities still exist, testifying to the close link between the Maltese inhabitants and the people of Rome. In AD 60, the islands were visited by Saint Paul, who is said to have been shipwrecked on the shores of the aptly-named "San Pawl il-Baħar". Studies of the currents and prevalent winds at the time however, render it more likely that the shipwreck occurred in or around Daħlet San Tumas in Wied il-Għajn.

After a period of Byzantine rule (fourth to ninth century) and a probable sack by the Vandals, the islands were conquered by the Arabs in AD 870. The Arabs, who generally tolerated the population's Christianity, introduced the cultivation of citrus fruits and cotton, and irrigation systems. Arab influence can be seen most prominently in the modern Maltese language, which also contains significant Romance influences, and is written in a variation of the Latin alphabet.

The period of Arab rule lasted until 1091, when the islands were taken by the Sicilian Normans. A century later the last Norman king, Tancredo di Lecce, appointed Margarito di Brindisi the first Count of Malta. Subsequent rulers included the Angevin, Hohenstaufen, and Aragonese, who reconstituted a County of Malta in 1283. The Maltese nobility was established during this period; some of it dating back to 1400. Around thirty-two noble titles remain in use today, of which the oldest is the Barony of Djar il-Bniet e Buqana.

In 1530, Holy Roman Emperor Charles V of Spain gave the islands to the Order of Knights of the Hospital of St John of Jerusalem in perpetual lease. (The Kingdom of Aragon had owned the islands as part of its Mediterranean empire for some time). These knights, a military religious order now known as the "Knights of Malta", had been driven out of Rhodes by the Ottoman Empire in 1522. They withstood a full-blown siege by the Ottoman Turks in 1565, at the time the greatest sea power in the Mediterranean sea. After this they decided to increase the fortifications, particularly in the inner-harbour area, where the new city of Valletta, named after Grand Master Jean de la Valette, was built.

Their reign ended when Malta was captured by Napoleon en route to his expedition of Egypt during the French Revolutionary Wars in 1798. As a ruse, Napoleon asked for safe harbour to resupply his ships, and then turned his guns against his hosts once safely inside Valletta. The Grandmaster, knew that he could only allow a few ships at a time to enter the harbour, due to the Treaty of Trent. Grand Master Ferdinand von Hompesch zu Bolheim capitulated, and Napoleon stayed in Malta for a few days, during which he systematically looted the movable assets of the Order, and established an administration controlled by his nominees. He then sailed for Egypt, leaving a substantial garrison in Malta.

The occupying French forces were unpopular, however, due particularly to their negative attitude towards religion. The financial reforms and the religious reforms did not go down well with the citizens. The Maltese rebelled against them, and the French were forced behind the fortifications. Great Britain, along with the Kingdom of the Two Sicilies, sent munitions and aid to the rebels. Britain also sent her navy, which instigated a blockade of the islands. The isolated French forces, under General Claude-Henri Belgrand de Vaubois, surrendered in 1800, and the island became a British protectorate, being presented by several Maltese leaders to Sir Alexander Ball.