No one was injured, as the terminal has not been in operation since the coronavirus pandemic began.
Footage has emerged on social media showing thick plumes of smoke and columns of fire billowing from the burning building that used to welcome international arrivals.
The airport is named after the village of Ignatyevo, located some 12 km north-west from the region's administrative centre of Blagoveshchensk, home to about 225,000 people.
Seven fire engines and several dozen firefighters were scrambled to extinguish the conflagration early Thursday morning local time.
Russia’s Emergencies Ministry reported that nobody has been injured in the incident, since the terminal was shut down due to the coronavirus restrictions that have brought international air travel to a screeching halt since earlier this year.
“An international section, which has been out of operation during the pandemic, has caught fire. There was nobody inside,” the airport’s officials told TASS.
The incident has not led to any flight delays or cancellations, with the airport’s operations believed to be unaffected by the fire.
It’s yet unclear what caused the blaze. In 2016 the airport was seriously damaged when a burning cigarette ignited trash, sparking a major fire.