Go to your local locksmith. Most have the "box" to program a remote. I paid 20 bucks for 1 remote.
Dealership
You have to program it with a DRB (Scan tool).
I had the same problem. Google "keyless entry remote 2003 Jeep Grand Cherokee".
dealer has to do it with factory scan tool
If you have 2 (a pair) it tells you in owners manual to program the 3rd. If you are programming a second, you will have to goto dealer so they can program it with drb3.
The only way to program keyless entry is with a very expensive diagnostic tool called "Launch" or go to nearest dealer for programming.
Remote start was not available on a 1999 Jeep.
how do you program your remote
The dealers scan tool is required.
How do i program my remote car starter / lawless remote
It is easy to do with online instructions. Just google "2004 Jeep remote programming"
You can just contact your local jeep dealership and they can get you a new one and program it for you. I belive that the actual remote is usually around $30 and it doesnt take that long to program so the labor shouldn't cost to much depending on the hourly rate.