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,M.V Malindo. 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). As of September 2019, your baggage is still being weighed and anything over 10 kilograms has to be paid for.
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. 10000 IDR (September 2019) is the minimum cost now for mikrolet in Nunukan. If coming in on the ferry from Tanjung Selor region, Indonesia, this ferry drops you off about 3 kilometers from the Nunakan to Tawau ferry terminal, motorcycle taxi cost 20000 from one terminal to the other terminal (September 2019) The Tanjung Selor ferry terminal is west of the main Nunukan to Tawau ferry terminal.
Ferry from Nunukan to Tawau. (September 2019). (Even the locals do not know the correct departures timings. Everyone you ask gives a different answer). However, one thing is certain - THERE IS NO FERRY SERVICE ON SUNDAYS! (Avoid the one million IDR fine for being one day over your visa limit). The first ferry seems to leave at around the 0830 to 0930 time (Sept 2019). In mid September 2019, the ferry ticket office opened at around 06:30 to 07:00. The ferry ticket office can be found inside the ferry terminal compound. Walk through the compound, after about 20 meters, turn RIGHT. The ferry office can be found in the building on your right (about 100 meters). The main terminal building (and immigration staff) is directly in front of the ticket office. The immigration procedure starts at 07:30. Departure tax is 15000 IDR. Payable as you enter the terminal building.