Cannot program keyfobs

I have 2 keyfobs that have worked for years. Recently they just stopped working. Naturally I think it is the battery. Nope. Tested each battery and they both draw at least 3V. Tried some new batteries just in case. I can easily get my car into programming mode following these steps (https://www.youtube.com/watch?v=zBgn6zSJkQs). But when I do the last step, pressing the lock & unlock, then unlock to connect the keyfobs, nothing happens. Any idea what the issue is? Thank you in advance!
 
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Have you checked your owner's manual? I had a similar experience and the instructions I had received were different than the manual. Mine is a gen 4 so I can't speak to the gen 3, but check your owner's manual for the proper sequence.
 
I recently couldnt program mine due to a clip not seated. was working on rear window and didnt fully seat one of the power clips in the door. thought the battery was dead in the fob. tried reprogram. didnt work. found the clip. then the fob worked fine.

maybe one of your door locks isnt actuating, which is required to allow fob to work. (I think) check and see if your doors actually lock and unlock when you press interior button, even hatch
 
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maybe one of your door locks isnt actuating, which is required to allow fob to work. (I think) check and see if your doors actually lock and unlock when you press interior button, even hatch
My rear hatch lock fails to lock automatically sometimes - so this is a real possibility. With a working fob, that means you don't get the beep confirmation - then it re-tries 1-2 seconds later. If it fails that second time, no beep. If you manually lock the hatch (with the key) within about 5 seconds, you will get the confirmation beep.

Cleaning and lubing the mechanism fixes it until the next off road trip, as does just working it back and forth with the key though not as reliably.

-Charlie
 
I recently couldnt program mine due to a clip not seated. was working on rear window and didnt fully seat one of the power clips in the door. thought the battery was dead in the fob. tried reprogram. didnt work. found the clip. then the fob worked fine.

maybe one of your door locks isnt actuating, which is required to allow fob to work. (I think) check and see if your doors actually lock and unlock when you press interior button, even hatch
The doors lock and unlock. What is weird is that both my keyfobs were not working. And my electric car charger also stopped working. I just ended up blaming it on the recent aurora that happened here in WA state. Got a nice show in the sky. :bounce:

I ended up just buying a new keyfob complete with circuit board and battery for $9 off Amazon. And using the same programming steps, I could immediately program the new keyfob.
 
I had the same issue when programing my eBay key fobs. I used the same video and scrolled down to read the comments. Turns out theres a different protocol where you turn it to the On position at the end, not the ACC position. Everything else is the same.

Here's the comment that helped me:
Okay, it ALMOST worked for me. I went and tried another YouTuber and you guys were just about equal in thought and procedure... except for ONE THING that will fail some owners of a 3rd Gen 4R. I literally tried your steps 22 times over a weekend period. I then gave up until...

This other procedure is identical until the last step. In his last step, he put the key in the ignition after the last 5-cycle lock/unlock... and then TURNED the key to the ON position (NOT starting or even clicking, just all the lights on the dash are lit), turned it back to off (still leaving it in), turning AGAIN to the ON position w/o starting; turn back to off and remove key. This is where I hear the locks saying, "Program mode!". Maybe this will help someone else with a similar situation. Had you heard about this before?

Also, at the end of all of this, you may get confused if your 4runner doesn't respond completely after all the lock/unlock cycles... especially if done at the switch inside. I actually had to wait a few minutes after the lock button quit working from ANY switches (door or FOB). Best save yourself 'now and future' problems by doing all this with the key in the door and bypassing the inside switch to prevent further wear and tear and possible future NOT functioning by being worn out. Just my FYI and experience(s).
 
I don't have any pics from when I did it, but a few years ago I wanted to program a new fob onto my '99, and couldn't get it to go into program mode. I'd done it successfully multiple times in the past (one time it was acting weird until I erased all the existing fobs and readded them again). But this time it just wouldn't go into programming mode, mostly due to it getting 'tired' from the repeated lock/unlock steps. The first attempt would be best, each subsequent one the locks were slower/more sluggish. Even helping the driver door lock using the knob wasn't working (that sometimes helps if it's a little weak).

Long story made shorter, I narrowed in on the door lock junction box, more specifically, the printed circuit part of it. It was far easier to replace just that part than to replace the whole box. I got a replacement from a 'nicer' junkyard 3rd gen of a close year (99+ for sure, not sure if they changed for 01-02) and it was fairly easy to remove and replace. And then the locks regained their pep, and it would easily go into programming mode. I removed all the existing fobs (presumably previous truck), added all the ones I had, still working great a few years later.
 
...wouldn't go into programming mode, mostly due to it getting 'tired' from the repeated lock/unlock steps. The first attempt would be best, each subsequent one the locks were slower/more sluggish. ...

Long story made shorter, I narrowed in on the door lock junction box, more specifically, the printed circuit part of it. It was far easier to replace just that part than to replace the whole box. I got a replacement from a 'nicer' junkyard 3rd gen of a close year (99+ for sure, not sure if they changed for 01-02) and it was fairly easy to remove and replace. And then the locks regained their pep, and it would easily go into programming mode. I removed all the existing fobs (presumably previous truck), added all the ones I had, still working great a few years later.

Holy guacamole...I am having the exact same issues!!! I can't enter program mode because the locks seems to struggle going up and down after a few tries, can't get all 5 cycles.

Thought about opening all doors and cleaning/greasing locks but perhaps I will try replacing junction box circuits first. Thank you!
 
Holy guacamole...I am having the exact same issues!!! I can't enter program mode because the locks seems to struggle going up and down after a few tries, can't get all 5 cycles.

Thought about opening all doors and cleaning/greasing locks but perhaps I will try replacing junction box circuits first. Thank you!

You can also help the driver door up and down using the knob, while using the button to lock and unlock. That helps if the motor in the door is a little weak. But in my case it was the body control module.

There are some pics in this thread: Body ECU test bad, or does it?

Replacing the whole module seemed to be a much larger task, LOTS of wires. But the circuit board just comes out pretty easily. In that thread they replaced a component (relay) on their board, I just got lucky enough to find one in a PnP junkyard that worked.
 

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