Nunukan  is a busy town on an island of the same name in North Kalimantan, bordering Tawau in Sabah, Malaysia. It serves as a main transit point to Tawau. Nunukan regency has 9 sub-districts: Krayan, Krayan Selatan, Lumbis, Sembakung, Nunukan, Nunukan Selatan, Sebatik, Sebatik Barat and Sebuku.
For visa requirements when entering Indonesia, see the Indonesia | Get in section. Note that Nunukan is not listed as a visa-on-arrival entry point. Visas need to be obtained before hand. Citizens of countries not needing visa to enter Indonesia can freely enter via this checkpoint.
Nunukan's Immigration office (Kantor Imigrasi) is about 200m from the port on Jalan Pelabuhan into town and opens at 8am.
To Tawau: Ferries link Nunukan to Tawau in the southeastern corner of Sabah, Malaysia. Tickets cost 200,000 IDR (March 2017, Update: 250,000 IDR now!) for one way. One departure scheduled daily at 9:00am (no ferry on Sundays!). The ferries operating are M.V. Tawindo Express, M.V. Mid East Express, M.V Labuan Express, M.V Mega Express', M.V Nunukan Express, and M.V Purnama Express, M.V Francis Express. There is a port tax of 15,000 IDR (March 2017, Update: rate remains the same) per person collected before departure. Journey time is about one hour. Ticket booths are opposite the port building. Be at the port one hour before the scheduled departure for immigration clearance. Be prepared to undergo a cursory health inspection on the Malaysian side and have some extra rupees ready for an additional baggage fee - your bags get weighed and everything over 10 kg costs extra (about 2 MYR / 7,000 IDR per kg).
To Tarakan: There is a Kalstar flight every two days (15 minutes, around 500,000 IDR), and numerous daily boats (3 hours, 260,000 IDR) at 9.00 a.m. (There might be an afternoon departure as well, but this could not be verified).
To/from other parts of Indonesia: Pelni  boats such as KM AWU,KM THALIA,KM BUKIT SIGUNTUNG KM UMSINI, KM DOBONSOLO and KM TIDAR,KM TILONGKABILA pass by Nunukan from cities in Nusa Tenggara, Bali, Sulawesi, Java and Kalimantan. Check with Pelni office in Nunukan (Add: Jalan. A. Yani 11, Tel: 0556-21309, 0556-21170, Fax: 0556-21029) for ticketing and departure time tables matters.
The cheapest way to travel around Nunukan is by mikrolet. These small minibuses running a fairly standard route and picking up and dropping off passengers anywhere along the way. You can get almost anywhere for Rp. 3.000 (Update: Been told 7,000 IDR nowadays but never tried, you try it out and confirm and update please :))