I have a 2000 Honda Accord with a factory installed alarm. When I press the button on the clicker it won't disable it. The light on the clicker lights up and the battery is fine. I've tried manually unlocking the door and even started the car and the alarm still keeps going off. What can I do?

I don't believe that the 1991 Accord DX had a Honda accessory alarm option, but regardless, factory or aftermarket, it was wasn't installed at the factory, it was installed at the dealer or an aftermarket store. Just remove it, and reattach any cut wires.

Getting into a car that has the security system by unlocking the door with the key will set the alarm off. Usually you can relock and unlock the door with the key and the alarm will be turned off. There are several things that can set off an alarm depending on the sensors, so do you have a remote key FOB and if so does it work. I am including a link to Honda Tech article that may help you out:
http://honda-tech.com/honda-accord-1990-2002-2/how-disable-factory-security-system-1638886/

Either unlock the drivers door with the key, or turn the ignition on and try to start the car. one or the other should disarm the alarm

Under the dash on driver side the alarm box is usually placed there. You should be able to unplug it from power there.

It appears to be a known issue!

https://www.google.com/search?q=2005+Honda+Accord+alarm+system+won%27t+turn+off

I would take it to a good vehicle electrician who has a good scan tool computer to test diagnostics on the whole electrical system.

On Accord - it does the same thing, but the solution is simple, don't hit the button the second time! It locks with just one push, the lights should blink to tell you. You don't need to push it twice if you don't want the horn to beep.

If the problem continued, You need to go to the honda dealer; factory alarms are wired into alot of the electrical systems, so, hard to bypass unless you have a wiring diagram.

Hope helped (remember comment and rates this) TY for using Fixya.

My ex girlfriend had a factory installed honda remote strt on her vehicle. It was activated by hitting the lock button two times in succession. Some vehicles use a combination of the lock-unlock buttons. try using some combinations on the remote, many "oem" remote starts are installed by aftermarket installers so who knows what they did as a start function, it could also have been changed by the previous owner.

try this...insert the key in the drivers door, turn left, then right and see if it resets the alarm

Blown fuse?, check to owners manual for a theft system fuse.

you would need to conntact the dealer it should run you around 30.00 for a new clicker takes 3 secs to set up the new one