The first domestic flight was from Malé to Gan on 28 December 2010. The airline began its international operations on 21 January 2011 between Hong Kong and Gan. The airline initially operated flights between Hong Kong and Gan once every 5 days. Later, the route was changed to Hong Kong and Malé, but continued the unique every 5 day pattern. The airline also began scheduled service from Malé to Shanghai on 16 July and to Beijing 22 July 2011.
Frequencies have increased since 2011 and the airline currently operates 4 to 5 flights a week to each of Beijing, Shanghai, and Hong Kong depending on the season. The airline has also served Chongqing, Chengdu, and Hangzhou, China as well as Incheon (Seoul), Korea, with seasonal services. The latest route to operate is from Hong Kong to Koror, Palau with twice weekly frequencies starting in mid-December, 2013.
The airline also provides technical services to other airlines at Male' Ibrahim Nasser International Airport including AOG support. The airline can also provide ground handling supervision and permit management services to other foreign airlines as well. The corporate headquarters of MEGA Maldives Airlines is located in Male', Maldives
In September 2016, MEGA Maldives announced it would cut 65 of its 400 staff as well as postponing planned new routes until further notice due to the severely decreased Chinese leisure market. In the same month, the airline introduced its first Boeing 737-800 on wetlease from Travel Service. The aircraft is part of its fleet modernization program and will be used for increased connectivity between short and medium ranged destinations, notably opening up new destinations in India and Sri Lanka.
Mega Maldives suspended all remaining operations on 2 May 2017 stating restructuring measures. Beforehand, it already significantly reduced its network down to only two Chinese destinations.