Thunderbird started in the early 1960s when it acquired the bush operations of Pacific Western Airlines in Prince George. From its base at Tabor Lake, Thunderbird operated Cessnas, Beavers and Otters on floats and skis servicing the new town of Mackenzie and the northern villages and logging camps of Williston Lake. In the early 1970s, Thunderbird secured a subcontract from Pacific Western Airlines to service the smaller communities of B.C. to feed that traffic into PWA's jet aircraft at Prince George, Kamloops and Kelowna. The need for a hangar on the Prince George Airport to fulfill this contract was the catalyst for the merger talks that resulted in the formation of Northern Thunderbird Air in 1971.
In the 1980s, the company had 18 aircraft, 3 bases, 21 scheduled points and numerous employees, but by the lare 1990s, the company had shrunk to 1 aircraft, 1 base, 2 scheduled points and 5 employees. NT Air has grown again to 10 aircraft, 3 bases, 7 scheduled points and 50 employees.
On October 27, 2011, a Beechcraft King Air, serial number B-36, registered C-GXRX, crashed on Russ Baker Way next to Vancouver International Airport in Richmond, British Columbia as it was attempting to make a landing, killing the pilot, 44-year-old Luc Fortin. It had departed the airport earlier but turned around due to indications of an aircraft malfunction (the engine oil pressure indicator); it crashed about 900 metres short of the runway. Five of the nine passengers were seriously injured. On November 16, 2011, the co-pilot of the flight died as well. 
Two pilots died in 2005 when a twin-engined Northern Thunderbird King Air 200 (BB-190, C-FCGL) crashed near Squamish when the plane was transitioning from Vancouver to Prince George. The pilot flew up a valley and was in a steep climb trying to avoid terrain when the plane crashed.
In 2001, a Northern Thunderbird single-engine Cessna 185 crashed north of Prince George while under government charter to do a wildlife survey. The pilot and passenger survived.