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Due to its location inside the Grand Harbour and the shelter offered by its creeks, Marsa has long been an attractive, welcoming and fruitful destination for visitors. Since Antiquity men searching for refuge have been cultivating the fields and growing crops here. The first port in Marsa has been established by the Phoenicians. Also, remains of Roman constructions have been found close to the town.

It is believed that a foundry of the Order of St John in Malta Order may have been located at Marsa. During the Great Siege of Malta of 1565, Marsa was used as a camp by troops of the Ottoman Empire. After their defeat, Marsa became a barony with a number of vineyards. An important bridge connecting the road from Birgu to Valletta was located here.

During the Middle ages and long after, il-Marsa belonged to the parish of St George at Citta Pinto, when in 1913 it was declared a parish. Since late 9th century, thanks to the activity in Portu Novu, the locality has grown into a suburb, despite the recent steady decline in population.

In the 17th century Giovanni Francesco Abela converts his house into a museum – the Museo di San Giacomo. Many of its artefacts are now kept at the National Museum of Archaeology in Valletta.

During the French blockade of 1798-1800, Maltese insurgents built Marsa Battery and Jesuit Hill Battery to encircle the French in the Grand Harbour, both of which were demolished after the end of the blockade.

A new port was constructed in the 1860s under the rule of the British Empire with the objective of creating the Albert Town, named after Prince Albert. Having reached a population of 600 people by 1890s, it was abandoned. The new town at the site emerged in the 20th century, taking the name Marsa after the creek.