Komodo International Airport is just east of town and has regular flights from Bali and Jakarta. The drive from the airport to the harbour area is short, often 10 to 20 minutes depending on where you are staying and how much traffic is backed up on the hill.
Overland travel across Flores is slow but rewarding. Buses and shared cars connect Labuan Bajo with Ruteng, Bajawa, Ende, and Moni along the Trans-Flores Highway, though the mountain road means distances take far longer than the map suggests.