Hello there.
I've just recently bought a 3rd generation 4runner. Mainly thanks to the informative posts in this forum.
Got myself a pretty well kept vehicle and everything seems to be in order, but there's something going on with the remote control.

When I press the lock doors button, most of the times nothing happens. I have to press around 5-10 times for it to work, same goes for unlocking.
Replaced the batteries but the problem remains.
I'm not sure if the problem lies with the remote or with the system itself, perhaps some of you can help me.

Thanks a lot!

It could be the switch contacts in the remote are worn.

Thanks a lot for the hasty reply. When I press the button the lights that are on the remote turn on though, could it still be because of the contacts? I'm guessing the two aren't related.

Quote-'I'm guessing the two aren't related."

I'll guess you are right on that. It's probably transmitting properly if the LED is nice and bright when you push the button.
This might mean the truck is not receiving the signal properly.
Try standing at different places around the truck including right in cab of the truck to see if there is any place where it works "every time".

On mine, ('97 Ltd) there is a small dipole antenna attached to the windshield behind the rear-vu mirror. Perhaps yours is damaged, missing, broken free and hanging somewhere ?
This would really decrease the sensitivity of the receiving unit.

Frankly, these things scare the crap out of me never owning a vehicle with a security system before. My whole trip resides in a small plastic remote control device that controls my ability to even start the truck.

I was under the impression mine was aftermarket but now I'm not so sure. I don't know how they are wired in. Mine has remote start as well. There is a sticker on the side window that give the mfgr/installer ?? but a web search did not turn up much.

If I could get rid of the anti-theft portion that would allow me to start it with a key if req'd, I'd be happy.

This gets us off topic a bit and sorry for that but have a look to see if you have some sort of antenna that receives the signal. As I said...not even sure if mine is "normal".

Have been messing around with the remote now. It seems like the truck is not receiving the signal correctly. I tried locking and unlocking from different places, but it just works randomly, I couldn't find a pattern. No idea what to do

I have similar troubles but with mine it locks every time but has the same symptoms as yours when it comes to unlocking or opening the rear window. My plan when better weather hits NH is to check the wires going into the rear hatch for damage. I've read on this site that there are wires that over time and repeated movement may cause the problem.