Established in July 2001 as a low-cost brand of Garuda Indonesia, it operates services to domestic and regional destinations.

Garuda Indonesia established Citilink as a low-cost brand in 2001 and operations commenced on 16 July that year with two Fokker F28 Fellowships transferred from the mainline fleet.

In 2008, Garuda temporarily suspended operations of Citilink, relaunching the brand in January 2009 after replacing the remaining Fokker F28s with more modern aircraft.

In late 2019, Citilink took delivery of two Airbus A330-900s originally ordered by WOW Air which are to be used for flights to Germany, Japan,[12] and Saudi Arabia.

[13] In June 2022, both Airbus A330-900s left the Citilink fleet and were transferred to Garuda Indonesia to complement the airline's Hajj operations.

[64] Citilink's first A320, a second-hand aircraft, arrived in late June 2011 and entered into service on 16 September 2011, linking Jakarta with Balikpapan, Banjarmasin, and Medan.

[69] On 16 January 2019, Citilink became the first low-cost carrier in the Asia Pacific region to offer Wi-Fi at 35,000 feet above ground for free using GX Aviation Systems.

[71] Citilink immediately took action by sacking the pilot involved in the incident and issuing letters of apology to affected passengers.

The ministry later added that the pilot had undergone drug testing, conducted by the Indonesian National Narcotic Agency.