Below are the instructions I just used to successfully reprogram a freshly cut transponder key blank I purchased on e-bay on my 4Runner. This method is supposed to work on 1998-2001 Models.
4Runner Key Programming
Add Duplicate Key
1.Simultaneously depress and release brake and accelerator pedals 1 time.
2.Insert master key into ignition
3.Within 15 seconds depress and release accelerator pedal 5 times.
4.Within 20 seconds depress and release the brake pedal 6 times and remove key.
5.Within 10 seconds insert new key into ignition.
6.Within 10 seconds depress and release the accelerator pedal 1 time.
7.After 80 seconds new key is registered and security light goes off.
8.Remove new key and depress and release brake pedal 1 time.
4Runner Key Programming
Add Duplicate Key
1.Simultaneously depress and release brake and accelerator pedals 1 time.
2.Insert master key into ignition
3.Within 15 seconds depress and release accelerator pedal 5 times.
4.Within 20 seconds depress and release the brake pedal 6 times and remove key.
5.Within 10 seconds insert new key into ignition.
6.Within 10 seconds depress and release the accelerator pedal 1 time.
7.After 80 seconds new key is registered and security light goes off.
8.Remove new key and depress and release brake pedal 1 time.