Getting to Brunei from Labuan and Kota Kinabalu

From Kota Kinabalu to get to Brunei can be done from air, sea and land. From land, there is a bus from Inanam Bus Terminal to Brunei at 8.00am which cost you RM100. The journey is 8 hours and there is one stop for lunch at Lawas. Same thing if you are from Brunei to Kota Kinabalu, the bus will depart at 8.00am at B$45.00.
Alternatively, you can take a ferry to Brunei which is also depart at 8.00am. However, there is a transit at Labuan for 2 hours. The total journey is 6 hours to reach jetty and additional 1 hour to reach Bandar Seri Bengawan. You probably will save 1 hour if to compare with a bus ride. RM68.60 for an all inclusive ferry fare for a Malaysian. Malaysian will get 50% discount off for the jetty fee only. Do not bother to survey prices for the ferry fare because same like bus, there is only one company doing this service. The ferry ticket can be purchased at Jesselton Point.
The good part about taking a ferry is not just the ferry is more comfortable and faster than bus but you got at least 2 hours to spend to visit Labuan! Labuan is a small island so you can drink and buy cheap liquor but remember that you are only allowed to carry one liter of liquor out from Labuan. Labuan is a tax free zone so that is why their liquor, cigarette and chocolate are very cheap.
You need to get to another ferry to Brunei at 1.30pm. Before you proceed, please remember to go back to the counter and pay RM10.00 to get a new ticket to board. Do not worry, RM10.00 is just the jetty fee. You are not purchasing a new ticket.
3 hours from Kota Kinabalu to Labuan and now additional 1 hour to reach Brunei. Finally, you will reach there approximately at 3.00pm.
To get to Bandar Seri Bengawan, there is a Muara Express Bus like this which is only B$2.00/way to get you there in 40 minutes. You will need to wait about 10 - 15 minutes after your ferry has arrived. Accordingly to the bus driver, he is purposely watching his time to make sure his bus is there to pick up the ferry's passengers once the ferry arrived. To get to jetty using this bus, you need to be at Bandar Seri Bengawan Bus Terminal at 6.30am, 11.30am or 2.15pm. No need advance ticket purchase. Alternatively, you can get a taxi at B$35.00/way.
There are two time slot to get back to Kota Kinabalu which is at 9.30am and 4.00pm. This is the ferry prices if you are travelling from Brunei to Labuan only. You need to purchase another ticket from Labuan to Kota Kinabalu which cost you RM24.20. The ferry schedule from Labuan to Kota Kinabalu is only at 8.00am and 1.00pm.
Queuing up for custom clearance. To foreigners, please do not be surprised why you got so many stamps when you are from Peninsular Malaysia <---> Sarawak <---> Brunei <---> Sabah. Even though Sabah and Sarawak is under Malaysia but they act like a country themselves. A good example is when you travel to United States, passing through Texas <---> Louisiana you need to present your passport and get stamped! 
Quite a dirty jetty. Anyway, I would like to summarize the total you are going to spend per way by using ferry is RM88.60 + B$2.00 which is way cheaper than taking a bus and you are able to make a short visit at Labuan. If the place in Labuan you planned to visit is a little to far to walk, you always can rent a car hourly at RM10.00 - RM25.00 per hour.
In my opinion if you are planning a day trip to Brunei, travelling from Kota Kinabalu is impossible. The only way is from Miri. 
Summary:-

By bus,
Journey overview: Kota Kinabalu <---> Bandar Seri Bengawan
Schedule: 8.00am
Price: RM100.00, B$45.00
Travel time: 8 hours
Good to know: Stop at Lawas for lunch break

By ferry,
Journey overview: Kota Kinabalu  <---> Labuan <---> Serasa Jetty, Muara (Brunei)
Schedule: 8.00am (from Kota Kinabalu), 9.30am and 4.00pm (from Brunei)
Price: RM78.60 (from Kota Kinabalu) , B$15.00 + RM24.20 (from Brunei)
Travel time: 6 hours
Good to know:
1) Transit at Labuan and the waiting time approximately 2 hours
2) If you are from Kota Kinabalu, the moment you reach Labuan head to the ticket counter straightaway to exchange ticket to Brunei.
3) There is a Muara Bus Express service from Serasa Jetty, Muara <---> Bandar Seri Bengawan at B$2.00/way.
4) If you want to reach Kota Kinabalu on the same day, you need to board the 9.30am ferry.

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