Sønderborg's small airport, eight kilometres north of town at Kær, has daily flights to Copenhagen with Alsie Express. Direct trains run from Copenhagen via Fredericia and Tinglev — the journey is a little over four hours each way. By car, Sønderborg is about three hours from Copenhagen and an hour and a half from Hamburg via the German autobahn and the small border crossing at Kruså.
The town is also a port for the small ferry service across the Flensburg Fjord to Germany in summer, useful if you are travelling by bike.