Firefly offers domestic flights from Penang to Langkawi, Kota Bharu, Subang, and to the international destinations Banda Aceh in Indonesia and Phuket in Thailand. Its flights from Subang serve Penang, Langkawi, Alor Setar, Johor Bahru, Kuala Terengganu, Kota Bharu and Singapore. Firefly operates the only scheduled passenger flights from Singapore's Seletar Airport, flying to its Subang hub using turboprop aircraft. The airline briefly operated jet aircraft in 2011, offering flights to Kota Kinabalu, Kuching, Sandakan and Sibu from Kuala Lumpur International Airport and internationally to Bandung and Surabaya via Johor Bahru. Domestically, the airline previously served an extensive intra-peninsula connection from its secondary hub in Penang to most major cities in Peninsular Malaysia. It discontinued flights to Kerteh, Kuantan, Ipoh and Malacca from Subang and Singapore. It also discontinued services to destinations in Sumatra and to the Thai Peninsula. The airline halted its planned expansion to Bengkulu, Jambi and Pangkal Pinang. In 2019, the airline has announced its interest to commenced a new operation to Betong, Thailand from its hub in Kuala Lumpur
Firefly started operations with two 50-seater Fokker 50 aircraft. It also took delivery of a third leased Fokker 50 aircraft to expand its services. On 26 June 2007, Malaysia Airlines signed an agreement for the acquisition of ten ATR 72-500 aircraft with options for ten more, to replace the Fokker 50s. The aircraft started to arrive from 11 August 2008, with five delivered in 2008, five in 2009, four in 2010 and the rest in 2011. All Fokker F50s retired by the end of 2008. On 25 August 2010, Firefly announced that it would take up four ATR 72s in the option clause of the purchase agreement. On 8 November 2010, Firefly announced an order for 30 Boeing 737-800 aircraft from year-end to 2015 as part of its expansion into east Malaysia initially, and into regional markets in the future. Firefly's first Boeing 737-800 arrived in December 2010 and began its operations on 15 January 2011. On 16 August 2011, Firefly announced that it would only operate the ATR aircraft from Subang and Penang, and cease its Boeing 737-800 and Boeing 737-400 flights. Jet operations were discontinued in accordance with a restructuring-of-services agreement made between Malaysia Airlines and AirAsia. On 16 September 2011, Firefly ceased the Johor Bahru – Kuching route. Other Boeing 737 services, including Kuala Lumpur – Kuching, Kuala Lumpur – Kota Kinabalu and Kuala Lumpur – Jakarta, were transferred to Malaysia Airlines in October 2011. On 18 December 2012, MASwings' parent company, Malaysia Airlines, ordered 36 ATR 72-600s for its subsidiaries. Twenty of the ordered aircraft will be delivered to Firefly while the remaining sixteen will enter service with MASwings.
