The fastest and most comfortable, but also the most expensive, Royal Brunei Airlines operates one or two daily roundtrip services between Kota Kinabalu and Bandar Seri Begawan. The flight takes about 40 minutes. Malaysia Airlines and its subsidiary MASwings no longer fly operate this route.

As of January 2010 there are two options for the road journey from Kota Kinabalu to Bandar Seri Begawan - road journey along route 1 in Sabah and route 1 sections 83 to 92, or by a ferry journey in Menumbok, a town about 80 km from Beaufort via route 1 and route 502 in Sabah. ^{[dead link]}. The car ferry is pricey but faster - advance booking is essential during public and school holidays.

By road all the way even in your own car is taxing, taking anything between seven and ten hours. A lot of time is spent waiting at border checkpoints, at Sindumin/Merapok, Mengkalang/Labu, Ujong Jalan/Pandaruan and Tedungan/Kuala Lurah, which can get very busy with long lines during weekends and holidays. There is also a ferry crossing which can take time too. The ferry crossing at Trusan, Lawas has been replaced with a bridge.

The journey is described in stages from Kota Kinabalu to Bandar Seri Begawan below. If you are traveling the other direction, just take the stages in reverse:

• Kota Kinabalu to Beaufort (92 km): The drive out of Kota Kinabalu is quite straight forward and well signposted. Road conditions are good and the road heading south from the city is a dual carriageway until reaching the Sabindo Intersection, where there are two possible routes to take - through Papar or around it. Going through Papar saves a few kilometres but are usually full of slow-moving vehicles or even congested during most hours. Taking the old road along route 1 is usually faster although the journey is longer. From this intersection the road becomes a single carriageway two-lane road. The two routes meet at the Benoni Roundabout about 8 km from Papar. The journey continues on route 1 and passes through quiet coastal towns like Kimanis and Bongawan, where it leaves the coast to head to Beaufort. Just before Beaufort a new road has been built to bypass Beaufort. This road can be accessed at the Bingkul Roundabout. You can leave or join this itinerary at Beaufort (see the Get in section above for details), where you can head to (or come from) Menumbok along route 502 (for/from Labuan or Brunei (via ferry)), Kuala Penyu along route 502 (for/from the Pulau Tiga National Park), or catch the train to/from Tenom. There are no border checkpoints along this stretch.

• Beaufort to Lawas (110 km): The longest leg in the journey, it also used to be the most difficult as there were long stretches of the road which were not paved. This has since changed and although not the best, a continuous ribbon of bitumen now links Beaufort to Lawas. From Beaufort, go onto the metal bridge (turn right if coming directly from KK) across the Padas River and proceed to Sipitang 58 km away. This stretch used to be unpaved but the road surface is now OK. You will pass the turn-off to Weston, a small seaside village which used to be the terminus of the North Borneo Railway. Sipitang, which clings along the beach, has quite a number of shops where you can break for a meal and several petrol stations along the road. The road swings inland heading towards the Sabah-Sarawak border at Sindumin 18 km away. At the end of the road is the Sindumin Roundabout where you should turn left. A smaller two-way roundabout named the Immigration Roundabout follows, reaching the Merapok/Sindumin Combined Immigration Checkpoint where immigration posts for both sides are found in a single building. As you leave Sabah, your passport will be stamped and your immigration card retained. Immediately after, at the other end of the booth (the Merapok side), submit your passport to Sarawak Immigration with a new immigration card to be stamped into Sarawak. (Going in the other direction you hand your passport and card into the Sarawak authorities who will return both to you and then you hand them into the Sabah authorities who will also stamp them and then return them.) This procedure may not apply to Sabah and Sarawak residents but check just in case. Following the checkpoint is a roundabout where the one-street town of Merapok lies. Instead of going straight to the town square, turn left at the roundabout. A road flanked by oil palm plantations goes the 35 km to Lawas. Just before reaching town, you will go onto a cable-stayed bridge across the Batang Lawas (Lawas River). You will also pass the junction to the Limbawang village of Long Tuma and Lawas airport. See Lawas page for more info on the town. Lawas is also a point where you can leave this itinerary (see Get in above) by heading to Bakelalan in the Kelabit Highlands.

• Lawas to Bangar (48 km): This stretch used to involve a ferry and border crossing, but immigration checkpoints and a new bridge have eliminated them. From Lawas, take the road out towards Trusan, about 20 km away. You will pass through a small complex on the right with shops and restaurants where the old checkpoint was located. Moving on will take you to the Mengkalap Immigration and Customs Checkpoint where you will need to get your passport stamped out to leave the country. Once through that, you need to carefully drive up a steep inclined road which suddenly drops at the other side just before the checkpoint. Adequate signs should warn you about it. You will then reach the Labu Temporary Checkpoint, the Brunei side of the border, where you will be stamped in to the country. From Labu, it's about 23 km easy driving to Bangar, Temburong's administrative center. The journey here is hilly and the air outside could be cold even on a fine day.

• Bangar to Limbang (20 km): This leg of the journey is short and should be relatively easy as traffic is light. It involves crossing two immigration checkpoints and one ferry ride at the border. From Bangar, head west on the main road. You will arrive at Puni where the old checkpoint, which is a wooden house and wasn't a drive-through facility, can be seen to the left at an intersection. Furthur down is the new Ujong Jalan Checkpoint, which is a drive-through checkpoint. Your passport will be stamped out of Brunei in preparation for your entrance back to Malaysia. After the checkpoint you will reach the Pandaruan River, the border of Temburong and Limbang. The ferry (RM8 or B$4) runs regularly and the crossing is almost ridiculously short. After landing on the Malaysian side, look out for the Pandaruan Checkpoint on the left as there is inadequate signage and blocks on the road to direct you there (the road passes by it). This is a drive-through facility although sorting out permits for cars may require you to park and get out of your car. From Pandaruan, it is a simple drive to Limbang just under 15 km away. You will pass Limbang airport just before entering town from the northeast direction.

• Limbang to Bandar Seri Begawan (60 km): To head towards the Brunei border at Tedungan, 43 km away from Limbang, you should head southwards out of town past the museum. The road, which is also the road to Nanga Medamit (the start of the Headhunter's Trail) runs parallel to the Limbang River. Take a right turn at the KM10 point (follow Nanga Medamit and Batu Danau direction) and travel for another 13 kilometres before taking another right turn. Going straight will bring you to Nanga Medamit. The road crosses the Limbang River at Batu Danau village and continues right up to the border checkpoint at Tedungan. Just before the checkpoint, there is a collection of shops and food outlets. They basically serve to quench the thirst of beer-starved people coming across from Brunei. Lines at the checkpoint can be phenomenally long, especially during weekends. Once you sort out Malaysian immigration and cross the border, you will immediately come to Brunei's Kuala Lurah checkpoint. Both Malaysian and Bruneian checkpoints have drive through lanes for you stamp your passport but you may have to get out of your car to sort out the necessary car permits. From Kuala Lurah, drive for 3 km to a roundabout near a petrol station. Here, follow the signboards to your destination. If you wish to head to the Bandar Seri Begawan city centre, turn right at the roundabout until you reach a set of traffic lights, then turn left. At the end of this short road turn right. Shortly after is the village of Kampung Bengkurong. Travel to the end of the road to find the main road and make a right at the traffic lights. This road will lead to the city. If you are heading to Miri or Kuching, turn left at the roundabout instead. At the next roundabout, turn right and go straight. You will pass through several kampungs. At the end of this road is the same main road as the route to Bandar Seri Begawan but at a different location. At this traffic light head left, then follow the signs to Jerudong, then to Kuala Belait.

This is one of the more comfortable ways of making the journey as you do not need to spend so many hours on the "road". The sea is also relatively smoother than traveling on the back roads of Sabah, Sarawak and Brunei (though on some days you may be in for a pretty rough ride). The ferries are not wheelchair-friendly. A person in a wheelchair can make the trip (seated in an airplane-like seat for the duration of the ride), but some very capable help will be needed as it involves a good deal of lifting, carrying and balancing.

Though there are several ferries taking the route between Kota Kinabalu and Labuan and Labuan to Brunei, if you take the wrong ones you may end up being stuck and forced to stay overnight in Labuan.

To get from KK to Brunei in the same day, the following is a possible strategy depending on the day:

• Since COVID, there is no longer a direct ferry from KK to Brunei or Labuan (Mar 2024).
• Take a direct bus to Menumbok, which will drop you off just opposite the ferry terminal.
• The speedboat from Menumbok to Labuan leaves every 1.5 hours, and takes about 20 minutes. It costs RM16 (as of 2024).
• Once in Labuan, you have the option to take the noon trip or the 3PM trip in which you'll have some time for lunch (and cheap beer!), shopping and perhaps a quick visit to the Labuan Museum, or maybe a cab ride to and from the Labuan War Cemetery.
• The ferry to Brunei leaves at noon most days, and at 9:30AM or 3PM on some days. It costs around RM60, and takes 1.5 hours (Mar 2024). You must pay a departure tax of RM10 at the ticket office.
• Once in Brunei, you'll go through immigration and customs at the Serasa Ferry Terminal. You can change money at the terminal. Then you board a shuttle to Bandar Seri Begawan. The shuttle costs B$2 and takes about 40 minutes to arrive at the bus terminal in BSB, in the southeast corner of the city.

From Bandar Seri Begawan to Kota Kinabalu, the following is the best game plan:

• Take the earliest express bus to the Serasa Ferry Terminal: it leaves at 6:30AM from the last bay in the bus terminal in Bandar Seri Begawan, which is next to the bay for Bus #39. It costs B$1, and the trip takes a quite random time (up to 2 hours including delay on departure), getting you to the ferry terminal just in time to buy a ticket for the 9:30AM ferry departure to Labuan. If you can't find the express bus, you can take bus 37/38/39 and transfer to bus 33; the travel time is similar and the price is also B$1. See Bandar Seri Begawan#By boat for details.
• The ferry to Labuan costs B$17 (B$15 + B$2 departure tax). Unlike the KK-Brunei direction, there is no two-ferry "package," nor can you book tickets in advance. You can change your remaining Brunei dollars to Malaysian Ringgit at the terminal. The ferry ride takes between 1 and 2 hours.
• When you arrive in Labuan, you will go through immigration and customs; immediately afterwards, go to the ticketing office (on the left after leaving the terminal facilities—not the ticket windows right outside immigration) and buy a ticket for the 1PM ferry, which is the last ferry of the day to Kota Kinabalu. This costs RM39 for lower deck ("economy"), RM44 for upper deck ("first class"). Now you have about an hour to explore Labuan and have lunch. There are some decent restaurants across the street from the terminal. There is a left-luggage facility. The cost is RM1-3 depending on size however there is no tourist information desk in the ferry terminal. Free Wi-Fi is available in the waiting room of the ferry terminal.
• The 1PM ferry arrives at the Point Jesselton Ferry Terminal in Kota Kinabalu at around 4:30PM. The terminal is an easy 20-minute walk from the center of town.

The easiest way to do it is the direct bus, which goes once a day in each direction and takes 6–8 hours. In Bandar Seri Begawan, it leaves from the waterfront near the main bus terminal at 8AM, but get there at 7:30 to buy the ticket. It costs B$45 (2019). From KK, it leaves from the KK bus terminal.

Below are more complicated (and therefore slower) variations, which may cause a delay in reaching your final destination.

• Kota Kinabalu-Lawas-Bangar-Bandar Seri Begawan:

Two possibilities:

Bus to Munumbuk - car ferry to Muara (http://www.pkljaya.com/Fares_Tickets.htm%5Bdead+link%5D) - public bus to Bandar.

KK to Lawas then Bandar ( same route as 1 but using a variety of transport)

If you are going the other direction, do the stages in reverse. Here is the stage-by-stage description

• Kota Kinabalu to Lawas: Catch an early bus or minivans from Kota Kinabalu either directly to Lawas or by breaking your journey in Papar, Beaufort and Sipitang. Sipitang Express Bus Sdn Bhd ^{[dead link]} has a 7:30AM express bus from KK to Lawas (RM20), taking about 4½ hours, allowing you to reach Lawas at about noon. The Lawas Bus Company express bus only departs KK in the afternoon and you will not make it to Brunei within a day. There are no direct minivans from KK to Lawas; you will have to at least change at Beaufort. If you cannot get direct minivans, you can change at Papar between KK and Beaufort, and at Sipitang between Beaufort and Lawas. Express buses leave from the Kota Kinabalu express bus terminal on Jalan Padang near the City Padang (City Field) in the city center whereas minivans leave from the open plot of land opposite Wawasan Plaza at the southern end of town. Minivans are most frequent early in the morning.
• Lawas to Bangar: You will probably have to do this leg by taxis -- one from Lawas to the Brunei border at Labu and one from Labu after you pass Brunei immigration to Bangar. Don't forget to get the taxi driver to stop at the Mengkalap Immigration checkpoint at Trusan (about 20 km from Lawas) just before the ferry so that you can stamp yourself out of Malaysia. There is no immigration checkpoint at the border. All this will of course turn out to be quite expensive. There may be minivans running up to Trusan or the border although they are not frequent. You could also try taking one of the rickety Lawas Bus Company buses from Lawas to Trusan but that will be as near to the border as you will get, leaving you only with taxis to continue the rest of the way to the border. Once in Brunei territory, taxis are your only option.
• Bangar-Bandar Seri Begawan: From Bangar, regular speed boats make the half hour journey to Bandar Seri Begawan. These boats leave from the jetty in town and bring you straight into Bandar Seri Begawan. An added benefit going directly from Bangar to BSB, instead of continuing to Limbang, is that it allows you to bypass going through two more sets of immigration checks.

• Kota Kinabalu-Lawas-Bangar-Limbang-Bandar Seri Begawan: This alternative is pretty much the same as the main itinerary; the difference is only at the Brunei end of the journey.
  • After leaving Lawas by taxi, instead of stopping at Bangar, you should continue by taxi from Labu to western Temburong-Sarawak border at Puni. At Puni, cross the Pandaruan River by boat or ferry and get stamped into Malaysia at the Pandaruan immigration checkpoint. From Pandaruan, you can catch a local bus or taxi to Limbang, about 15 km away.
  • Once at Limbang, head to the jetty and catch a speedboat to Bandar Seri Begawan, which should take about half an hour. These boats leave when full and they are more frequent in the morning. However, if you have come directly from Kota Kinabalu, you may just make it for the last boats at about 4:30PM.
  • If you miss the boat connection, you can catch a bus or taxi to the land border crossing at Tedungan (bus destination "Batu Danau") 43 km away. After clearing Malaysian and Bruneian immigration (the checkpoint is called Bukit Lurah on the Brunei side), catch the purple minibuses to Bandar Seri Begawan. These buses (B$1) operate til about 7PM and the journey is about half hour.

• Other variations:
  • Kota Kinabalu-Lawas-Bandar Seri Begawan: There is a daily Lawas-Bandar Seri Begawan ferry but they leave very early in the day. If you are coming directly from Kota Kinabalu, you will have to stay the night in Lawas if you want to catch the ferry. The only reason why you may consider this option is to avoid the expensive taxi ride from Lawas to Bangar in Brunei's Temburong district. Indeed, with cheaper accommodation options in Lawas, you may end up spending less by spending the night in Lawas. Also, you will only deal with one set of immigration checks - once by the Malaysians when leaving Lawas and then by the Bruneians when arriving in Bandar Seri Begawan.
  • Kota Kinabalu-Lawas-Limbang-Bandar Seri Begawan: There is a daily ferry between Lawas and Limbang but again, they leave early in the day, requiring an overnight stay at Lawas. Once in Limbang, there is plenty of time for you to catch the direct speedboat, or do the road trip, to Bandar Seri Begawan. This option allows you to skip the expensive taxi rides between Lawas and Bangar while still get to see the geographically unique outpost of Limbang. Again, you will only need to go through one set of immigration checks - either at Limbang Wharf and Bandar Seri Begawan jetty if you take the speedboat, or at Tedungan-Bukit Lurah if you go overland.