Wakkanai is the northernmost airport in Japan which is capable of handling jet aircraft; due to its small size, it is susceptible to closures during the coldest winter months, in which case incoming aircraft are often diverted to Asahikawa Airport. It has one jet bridge, one apron gate for mid-sized jet aircraft, and two apron gates for commuter aircraft.
In 1987, the 1,200 m main runway was extended to 1,800 m, allowing All Nippon Airways to begin jet service to Tokyo. The flight was initially seasonal and did not become a year-round service until 1997. The city of Wakkanai provided subsidies for city residents to use the flight until 2005, when discounted fares became available.
As of 2015, ANA has two scheduled daily round trips to Sapporo using Bombardier Q400 turboprops, and one scheduled daily round trip to Tokyo (two from June to September) using Boeing 737 jets.
The airport is located on Japan National Route 238 approx. 12 km from central Wakkanai. There is regular bus service to Wakkanai Station and Wakkanai Ferry Terminal, timed to coincide with ANA flight schedules.
Until 1989, the JNR Temboku Line passed by the airport; however, the airport did not have a station on the line except for one day in June 1987, when a temporary Higashi-Koetoi Station was opened to accommodate visitors to the airport's extended runway.