The company was set up with the name of Alisarda on 29 March 1963 by Aga Khan Prince Karīm al-Hussaynī with the aim of promoting tourism in Sardinia.

During the year, further important investments were made aiming to develop Meridiana, which also closed 2006 with the historical record of 4,6 million passengers carried with an approximate 15% increase compared to 2005.

At the end of February 2010, Meridiana fly, the second-largest carrier in Italy, was created by the merger of Eurofly, a company specialized in long-haul charter flights to holiday destinations, and Meridiana, a scheduled operator of national and European flights, with the primary objective of connecting the main Italian airports with Sardinia and Sicily.

In mid-2013, Meridiana offered national and international scheduled flights from the main Italian airports to Sardinia (Olbia, Alghero, and Cagliari), Sicily and Naples as well as holiday destinations such as the Canary Islands, Greece, and the Red Sea.

It also serviced the long-haul destinations of the Maldives, Mauritius, Kenya, Zanzibar, Santo Domingo, and Brazil mainly from Milan Malpensa and/or Rome Fiumicino.

In 2014, the airline continued to reposition its brand by launching international flights to Moscow Domodedovo, London Gatwick, Kyiv, Tel Aviv and Nice from Naples and to Brussels, Geneva, London Gatwick, Tel Aviv, Nice, Hamburg, Paris CDG, Moscow Domodedovo and Kyiv from Olbia; reconfirming its leadership in Sardinia and its focus on Naples, Catania, Milan Linate and Verona airport for domestic Italian flights.

Since 18 November 2014 Meridiana Club frequent flyers have been able to earn Avios points on British Airways and from 23 March 2015 on Iberia.

In December 2014, Meridiana retired its last Airbus aircraft, two A320-200s, to pursue the aim of operating an all Boeing fleet together with Air Italy.