There are daily flights from Makassar (Ujung Pandang) International Airport to Baubau. Wings Air/Lion Air offers 2 flights to and from Baubau, one in the morning and one in the afternoon.
Garuda Indonesia offers 1 flight daily between Makassar and Baubau.
You can get to Makassar direct from Jakarta, Bali, and many other cities in Indonesia. You can also take Air Asia direct from Kuala Lumpur, Malaysia to Makassar.
The PELNI (National Cruise Service in Indonesia) provides service from east to west Indonesia through Baubau multiple times per month.
The Cantika speed boat travels 2 times a day between Kendari and Baubau, and is about a 5 hour boat ride one-way.