The airport was originally constructed by the United States Navy during World War II for the purpose of testing defogging systems for aircraft. In December 1947 a Southwest Airways DC-3 flying into the airport made the world's first blind landing on a scheduled commercial airliner using Ground-Controlled Approach (GCA) radar, Instrument Landing System (ILS) devices and Fog Investigation and Dispersal Operation (FIDO) oil-burning units adjacent to the runway. By the following year the airline had made 1,200 routine instrument landings at the often fog-shrouded airport.

For the year of 2005, the Arcata-Eureka Airport serviced 102,000 arriving commercial passengers and 104,000 departing on 4,370 departing flights. Horizon carried 66.29% of the passengers with United carrying the remainder. 78% of the 2005 flights departed on time and 79% of the arriving flights were on time. In addition to passenger traffic, the airport also shipped 457,000 pounds (207,291 kg) of cargo.

Current utilization is now a mixture of general and commercial aviation with two commercial airlines providing scheduled service: United Express operated by SkyWest Airlines, and Horizon Air.

The Arcata-Eureka Airport covers 745 acres (301 ha) and has two runways:

Being located on the Pacific coast of California, the airport falls under the jurisdiction of the California Coastal Commission and major changes to the airport such as rezoning or fencing in the airport require approval by the Commission.

The approach flight path for runway 32 passes over Central Avenue, a highly travelled road in the area. The strobe lights that direct planes onto the runway were creating a visual hazard for drivers on Central Avenue as the strobe lights were creating a glare. The problem was especially noticeable during inclement weather when the strobes' intensity was increased and the roadways were reflective from water on the surface. The Federal Aviation Administration's Office of Aviation Research, Airport Technology Research and Development Branch responded to the hazard by installing baffles on the strobes that block the lights from shining on the road while still providing visual guidance for aircraft.