I hiked Mt. Santubong at the end of August, in the middle of the week. It took me about 6 hours total (up and down, including a long break at the top and a couple of dips in the waterfall). The only other people I saw the whole time was a lone French guy, and a group of Malaysian teachers. Other than that, I had the whole mountain to myself.
From what I understand, there are two main access points to climb to the summit. Coming from Kuching, the first one is Bukit Puteri (Princess Hill), and the other is The Green Paradise Cafe (where I started). If you start at Bukit Puteri, apparently it's free, but from the Green Paradise Cafe, they charge you a fee of 8 ringgit (not a big deal, but more than free). They have a locked gate, so that only people that pay the fee can enter/exit at the cafe.
I had planned to start at Bukit Puteri, but the shuttle driver said I should start at the cafe. His English wasn't very good, so I didn't know why he was suggesting it, but possibly he gets a cut from the cafe for everyone he drops off there (just a guess). Anyways, I would recommend starting at Bukit Puteri, but either on the way up or the way down, do a side-trip onto the Green Paradise Cafe trail (maybe 10-15 minute walk) to the waterfall, so you can go in for a dip.
Whichever route you choose, you're doing a lot of very steep hiking, with a few sections of rope ladders. It's a really nice hike, though, and the views from the top are outstanding!
I think I read somewhere that the clouds often move in in the early afternoon, and the day I did it, I got to the top a little after 1pm, and the clouds were indeed slowly moving in. I started hiking about 10am, and so if you can start earlier, you might increase your chances of having good views.
I saw several frogs, lizards and I almost stepped on a huge snake. It was just sitting in the middle of the trail, and I guess I surprised it. It was almost 2 metres long (maybe 5 feet), but when it noticed me, it took off like a rocket into the bush. I met an American guy during my stay in Kuching who said he'd seen proboscis monkeys at the top of Santubong, so you might get lucky.
I caught a shuttle from Kuching (I paid 10 ringgit). I just went to the desk at the Grand Margherita Hotel (near the east end of the riverfront) and they had the shuttle driver come talk to me. On the way back to the city, I flagged down a bus (Citylink, I think) and they wanted 10 ringgit to get back to the city. I'm sure that was going straight into the driver's pocket, as the bus fare should only be 4 or 5 ringgit, but my alternative was to wait an hour or so for the shuttle and pay 10 ringgit anyways.
If you're in pretty good shape and love hiking, I highly recommend Mt. Santubong, but make sure you've got lots of water and some snacks, as it's quite a workout.
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