There are 3 options for getting between Bander Seri Begawan and Kota Kinabalu. Flying, ferry or bus.
1 – Fly
Check out skyscannet.net for prices
2 – Ferry
From Bander Seri begawan to the ferry terminal, Serara Ferry Terminal, there is around 30km. Getting there takes a couple of busses or a taxi. The taxi will cost around $30-40 Brunei dollars ($21-29 USD). We have been told there is no need to book here as there are plenty of space. The ferry leaves at 09.00 arrive at 11.00 to Labuan ferry terminal, price $17.00 Brunei dollars ($12.40 USD).
From Labuan to Kota Kinabalu another ferry is needed, leaving at 13.30, arriving to Kota Kinabalu at 16.30. The price is around 50 MYR ($11.60 USD).
Total price for ferry ~ $50 USD pp , of course the price comes down depending on how many share the taxi
3 – Bus
Busses leave from downtown Bander Seri Begawan at 08.00 daily. The price is $45 Brunei dollars ($33 USD) if booking from the agency in town, or $25 USD if booking online at www.easybook.com this is slightly cheaper at it’s a Malaysian company. At the moment there is a discount code, easy321 for 20%.
Note, when taking the bus you will get 8 stamps on your passport. As leaving Brunei twiwe, entering Malaysai twice, as well as crossing terrority in Malaysia from Sarawak to Sabah. Officially 2 blank pages in a passport is needed to enter Brunei, don’t know if this is upheld
Total price for the bus ~ $25 USD pp