- Kupang — the capital of East Nusa Tenggara province and the island's transport hub.
- Atambua — a city near the border with West Timor (Timor Leste).
- Kefamenanu Kefamenanu is the capital of North Central Timor regency. The regency is in the middle of Timor island. There are many interesting places like the traditional village of Tamkesi, Taolin palace, and some natural caves. The culture is maintained well by the people and is also of interest to some visitors. As the capital city of the regency, Kefamenanu has hotels, travel services, hospitals and a university.
- Soe — the capital of South Central Timor regency. Being in the mountains, it is significantly cooler than in the coastal regions.
There are no flights from East Timor, so crossing the island involves an arduous 12-hour trek by bus to Kupang. A short bus called Gemilang with about 30 passengers connects Dili, Timor Leste with Atambua. Passengers are picked up at home and disembark at the destination.