Flights arrive at Ufa International Airport (http://www.airportufa.ru/...) IATA: UFA. There is at least one flight a day to Moscow and to St. Petersburg. There are also flights to Turkey.
Airport lies southeast of the city and not so far from the city center. A taxi from the train station to the airport takes about 25-35 minutes and can cost $15-25. Public transportation to and from the airport is uncomplicated, as there is direct bus service between the airport and the city center.