Construction of the airport started in 1970. It opened for operations in 1980.

In 2005, the airport launched Terminal 2 for handling transit and international passengers. By 2006, the old runway coating had been replaced by an asphalt-concrete layer with reinforced polymeric netting.

In November 2007, it was announced that Lufthansa Cargo might switch its Asian refueling and distribution point from Astana, Kazakhstan, to Krasnoyarsk (Yemelyanovo) International Airport, because Russia would no longer permit Lufthansa the use of its air space for their Europe to Asia flights unless they could sell fuel. In July 2008, Lufthansa stated that it would move its cargo logistics hub from Astana to Krasnoyarsk (Yemelyanovo) once the airport was brought up to ICAO safety standards. The cargo terminal of Lufthansa Cargo in Krasnoyarsk (Yemelyanovo) airport was its second largest one after Frankfurt. However, in October 2016, Lufthansa Cargo switched all flights from Krasnoyarsk (Yemelyanovo) to another Siberian airport Tolmachevo (Novosibirsk) citing its better infrastructure and the ability to outsource certain services whereas in Krasnoyarsk the company “had to involve its own personnel and equipment”. On the other hand, AirBridgeCargo Airlines switched its activities vice versa from Tolmachevo Airport to Yemelyanovo in January 2018.

In 2008, the modern arrivals terminal with the capacity of 750 passengers per hour was opened. Also in 2008, the lighting facilities were reconstructed and the new hi-intensity lighting system was installed: the centerline lights and the touchdown zone lights. In 2011, the airport handled over 1.6 million passengers, a 28% increase over 2010.

In November 2017, the general director of the airport announced that the airport will now be called Krasnoyarsk-International, instead of Krasnoyarsk-Yemelyanovo. It is unknown if the airport has as yet been officially renamed.

Before 2019, RZD made a decision to construct a railway line to the airport, but due to escape of high ticket price and small train occupancy, this will not be an Aeroexpress route, this will be a simple commuter service. Nevertheless, the route will also serve cargo trains, to deliver air-cargo goods directly to Krasnoyarsk.

In March 2019, Aeroflot signed an agreement with the government of the Krasnoyarsk region and Yemelyanovo Airport to create a local international hub. The project will start in 2020. On 31 May 2021, Aeroflot officially commenced its hub operation in Krasnoyarsk.