The airline was established in 1995 as a response to the commencement of discount services between Australia and New Zealand by Kiwi Airlines and started operations on 8 December 1995 with a single Boeing 757-200 which was leased from Britannia Airlines, UK. It was formed as South Pacific Air Charters by Mount Cook Airline. It is now wholly owned by Air New Zealand.
During 1998 a Boeing 737-200, ex Air New Zealand mainline fleet, was added to the fleet and the Freedom Air route system was expanded. In 2000 the B752 and B732 were replaced with three Boeing 737-300 aircraft, also ex Air New Zealand, and the routes were further expanded to provide a bi-weekly service to Nadi in Fiji. The flights to Fiji were discontinued late in 2000 following the military coup there.
By 2004 its fleet had expanded to five Boeing 737-300 aircraft and Freedom Air was providing direct non-stop services to the Australian cities of Brisbane, Gold Coast, Sydney and Melbourne from Hamilton, Auckland, Wellington, Christchurch, Dunedin and Palmerston North. Freedom briefly operated on the New Zealand main trunk domestic routes such as Auckland-Christchurch, but ceased these services to concentrate on providing value trans-Tasman flights.
In 2006 the B733s were merged back into the Air New Zealand fleet and all trans-Tasman flights were serviced using the newly acquired Airbus A320-200 aircraft. The majority of the A320 fleet were painted in the Air New Zealand livery and these were often seen operating Freedom sectors. Two of the A320s were painted in the 'Freedom Yellow', ZK-OJK and ZK-OJL. The latter sporting the very colourful 'Warner Brothers' mural.
At the end of March, 2008 Freedom Air was absorbed into Air New Zealand and ceased to exist as its own entity. The Freedom international routes, with the exception of the Palmerston North services, were all taken over by Air New Zealand. Palmerston North does not now have any international movements.