If you’ve recently bought a keyless remote entry fob for your Honda or the battery died in your existing remote, programming it is quick and easy.  There’s no need to take the remote to a dealership for programming, simply follow these 9 simple steps.
A Step by Step Guide for Programming Your Honda Remotes

Step 1:  Gather all the Auto Key Programmer.  You only need one remote to access program mode, but all remotes must be programmed during the same session.  Your Honda will “forget” any remote previously programmed.

Step 2:  Sit in the vehicle with all the doors closed and unlocked.

Step 3:  Turn the key to the ON position, one click before starting the ignition.  The lights on the accessories should come on and the dash will light up.

Step 4:  Within 5 second of turning the key to the ON position, press the LOCK button on your remote control transmitter for one second.

Step 5:  Turn the key to the OFF position.

Step 6:  Repeat Steps 4 & 5 two more times for a total of three ON/OFF cycles.  Each step must be done within 5 seconds of the previous step.

Step 7:  Turn the key back to the ON position (this will be your fourth turn of the key), press the “LOCK” button on your remote.  The Honda Key Programmer locks on your Honda will make a clunk noise exactly as they do when locking.  You doors have not locked.  This noise indicates your Honda is now in Remote Programming Mode.  Do not turn the key off.

Step 8:  If you would like to program more than one remote, press the LOCK button on each additional remote for 1 second.  As with all other steps, you have 5 seconds to complete this step.  Programming Mode will be activate for a total of 10 seconds.  Only 3 remotes can be programmed to each Honda.

Your locks will make the clunking noise (as though the doors have locked) after each remote is programmed to indicate they have been successfully stored in the system’s memory.

Step 9:  Turn the key to the OFF position and remove it from the ignition.  Test all of your remotes to ensure they have been successfully programmed.

Remember that your remote will not work if the key is in the ignition.  If you’ve lost your keyless entry remote, it’s a good idea to reprogram your Honda remote to protect your vehicle from theft.