I have successfully reprogrammed my remote entry fob (not the key) for my 2004 T4R OEM fobs and for a fob purchased off Amazon. It took several tries. You have to be persistent and follow the instructions exactly.

I have a link to a site for doing this. Not all model years can be done.
2004 Toyota 4Runner Remote Programming – Free Keyless Entry Remote Key Fob Programming Instructions

I am attaching a picture and a pdf with instructions. I think they are the same but from different sources.

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2004 Toyota 4Runner Remote Programming.pdf (93.9 KB, 97 views)

So does the reply on the second page work to delete previous fobs or do we have to take it to the dealer? I'd like to clear all fobs and reprogram the ones I have into the system. I was able to add 2, but not my third fob.

Using this step from the instructions for my 2004 T4R I was able to change the code and recode 2 fobs, an OEM and a new one from Amazon. It took several tries with the first two but eventually I got them both coded.

In the meantime the person who took my keys has returned them so I need to code the second OEM fob with the code from the first 2. I tried the returned fob and it didn't open the doors or lower the rear window, so I know it changed the code. Now to see if I can just add the 3rd one back to the group.

Switch ignition ON and OFF once to program a remote transmitter code whilst
retaining the original codes or twice to program a remote transmitter code
whilst erasing the original codes. Three times to check how many remote
transmitters are currently registered or five times to erase all registered codes.

The key thing works. Was able to erase all current fobs and then I reprogrammed the two I had, however, it still doesn't want to accept one so I'll just junk it. I have a 2008.

If it's an OEM fob you might post it for sale. After market fobs aren't too expensive but OEMs are worth some money. Ask your local dealership for a price. I have to reprogram a 3rd remote fob so I'll see if my 2004 will let me do that. If not, I'll delete all of them and program the OEM fobs.

I have 4 sets of keys for a 2012 Corolla. I lost 2 original sets in the house, but had the courtesy key. I had a locksmith create a new master from the courtesy key. Then I found the lost 2 sets and he reprogrammed all of them again, but he had some kind of laptop-like device that I had to pay $25 for him to use (he said it was some kind of payment he had to make whenever he used it).

All 4 keys will start the car and open the trunk, including the courtesy key (he cut that one to do this). The 3 keys with built in remotes will all unlock the doors. Good locksmiths can do just about anything.

i had bought a pair off of ebay $8 that didnt work no matter what i tried....

i purchased ones off of amazon $20ish under keyless2go and they programmed after the 2nd try.

yay!!! finally keyless, next thing fix the rear window.

I got mine from USA Remote last November for $15 and like you, it took 2 tries. Then the first week of this month whoever took my keys last September (by accident?) returned them to lost and found at the gym. They had them for 8 months. I guess the weather had to get warmer so they could put on a lighter jacket and find my keys.

After struggling for hours to program my key FOB myself, I knew I had to get some help. That's when I found Corefy's Key FOB Programming service. They were so knowledgeable and helpful, and the process was so easy! Corefy Forex payment processing solution and merchant account • Corefy Key FOB Programming service saved me a lot of time and hassle. Highly recommend!