Nine departures and the same number of arrivals were cancelled to and from Arlanda Airport, Bromma Airport and Gothenburg Landvetter Airport, said Swedish airport operator Swedavia.
Four departures from Denmark's Copenhagen Airport, the main hub for people flying in and out of southern Sweden, were also cancelled.
THE LOCAL GUIDE: What are my rights if a flight is cancelled or delayed?
Belgian air traffic controllers walked out at 10pm on Tuesday for a 24-hour strike called by three major trade unions in a wage growth dispute, causing all flights in and out of Belgium to be grounded.
No planes are allowed to fly lower than 8,000 metres in Belgian airspace during this time, as a security measure because staffing levels during the industrial action cannot be guaranteed.
European air traffic controllers Eurocontrol said it would publish “some advisory routings to avoid Belgian airspace”. In Belgium, passengers were asked not to come to the airports on Wednesday.
You can read more about your rights as a passenger in the event of strikes here.