In 1943, the Pocatello Army Airfield was built as a Second Air Force heavy bomber (B-17, B-24) training base. By 1949, the new airfield had become a surplus property and was obtained by the city of Pocatello to build a commercial airport.

While the starting date is unknown, Western Air Lines served Pocatello for a number of years, but discontinued all service by 1980. According to the airline's August 1, 1968 system timetable, Western operated Lockheed L-188 Electra turboprops into Pocatello. In September of 1973, this service was replaced with the new and more efficient Boeing 737-200, which offered nonstop flights to Salt Lake City, Las Vegas and Los Angeles. After discontinuing mainline flights, the airline subsequently served the airport as Western Express which was operated as code share service by SkyWest with commuter turboprop aircraft. Western merged with Delta Air Lines in 1987, and SkyWest continues to operate the code share service as Delta Connection.

In the mid 1970s, Hughes Airwest served the airport with Douglas DC-9-10 and DC-9-30 jetliners, according to the February 1, 1976 edition of the North American Official Airline Guide.

In the mid 1980s, Cascade Airways served Pocatello with British Aircraft Corporation BAC One-Eleven twin jets, according to the February 15, 1985 edition of the North American Official Airline Guide (OAG). The OAG also lists Cascade flights operated with smaller Fairchild Metro commuter turboprops.

Horizon Air served Pocatello until January 7, 2006, originally with service to Salt Lake City in 1983. The airline canceled that service in favor of flights to Boise starting in 1984 operated with de Havilland Canada DHC-8 Dash 8 turboprops.

Big Sky Airlines served Pocatello from the day Horizon canceled service until March 30, 2007.

In 2014, a World War II-era mortar was found on the airport grounds while doing routine maintenance work. The mortar was safely removed by law enforcement.

In 2024, NASA retired their Douglas DC-8 from the fleet, before retiring, NASA flew across the United States and landed in Pocatello, and is still currently restored there. This Douglas DC-8 was one of about 3 total aircraft that were still flying at the time. The DC-8 was donated to the airport for education use for Idaho State University. The aircraft sits next to the taxiway and general aviation parking area of the airport.